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> | 2011 News 2010 News 2009 News 2008 News 2007 News 2006 News 2005 News 2004 News 2003 News 2002 News 2001 News 10 October 2011 - Updated Yeast Browser Released We are happy to announce the release of an updated browser for the Saccharomyces cerevisiae yeast genome. The April 2011 sacCer3 assembly corresponds to the S288c assembly produced by the Saccharomyces Genome Database (SGD) project. For more information on this genome, see the SGD Genome Overview. full Downloads of the yeast data and annotations may be obtained from the UCSC Genome Browser FTP server or Downloads page. We'd like to thank the SGD for providing this genome assembly. The S. cerevisiae Genome Browser and annotation tracks were produced by Hiram Clawson, Greg Roe, and Steve Heitner. See the Credits page for a detailed list of the organizations and individuals who contributed to this release. 8 September 2011 - New Navigation and Display Features We've added several new features to the Genome Browser that make it easier to quickly configure and navigate around in the browser's annotation tracks window. Automatic image resizing: The first time the annotation track window is displayed, or after the Genome Browser has been reset, the size of the track window is now set by default to the width that best fits your Internet browser window. If you subsequently resize your browser window, you can automatically adjust the annotation track image size to the new width by clicking the resize button under the track image. The default width can still be manually overridden on the Track Configuration page. Scrolling left or right in the track window: You can now scroll (pan) horizontally through the tracks image by clicking on the image, dragging the cursor to the left or right, then releasing the mouse button. The view may be scrolled by up to one image width. Improved drag-zoom navigation: The browser's "drag-and-zoom" feature lets you quickly zoom to a specific region of interest on the annotation tracks image. To define the region you wish to zoom to, click-and-hold the mouse button on one edge of the desired zoom area (which can be anywhere in the tracks window), depress the shift key, drag the mouse right or left to highlight the selection area, then release the mouse button. The annotation tracks image will automatically zoom to the new region. The Genome Browser still supports the earlier implementation of this feature, which restricted the click-drag to the Base Position track area of the image, but did not require the shift key to be pressed. Reordering groups of tracks: You can now vertically reposition an entire group of associated tracks in the tracks image (such as all the displayed subtracks in a composite track) by clicking and holding the gray bar to the left of the tracks, dragging the group to the new position, then releasing the mouse button. To move a single track up or down, click and hold the mouse button on the side label, drag the highlighted track to the new position, then release the mouse button. If you haven't yet tried the browser's right-click menu for quick access to frequently used track configuration features and functionality, read more here. 18 August 2011 - New Feature: Track Data Hubs We are pleased to announce a new feature in the UCSC Genome Browser: Track Data Hubs. Track hubs are web-accessible directories of genomic data that can be viewed on the UCSC Genome Browser alongside native annotation tracks. The Track Hub utility allows efficient access to data sets from around the world through the familiar Genome Browser interface. Browser users can display tracks from any public track hub that has been registered with UCSC. Additionally, users can import data from unlisted hubs or can set up, display, and share their own track hubs. The data underlying the tracks in a hub reside on the remote server of the data provider rather than at UCSC. The data are stored in compressed binary indexed files in bigBed, bigWig or BAM format that contain the data at several resolutions. When a hub track is displayed in the Genome Browser, only the relevant data needed to support the view of the current genomic region are transmitted rather than the entire file. The transmitted data are cached on the UCSC server to expedite future access. This on-demand transfer mechanism eliminates the need to transmit large data sets across the Internet, thereby minimizing upload time into the browser. To check out some track data hubs that are already available, most notably those from the NIH Roadmap Epigenomics Mapping Consortium, press the "track hubs" button in the genome browser, or follow this link: http://genome.ucsc.edu/cgi-bin/hgHubConnect. To read about using hubs, or creating your own, see the User's Guide. 16 June 2011 - Re-engineered OMIM Tracks Released We announce today the release of our newly re-engineered OMIM (Online Mendelian Inheritance in Man) tracks for both hg18 and hg19. With the kind assistance of Ada Hamosh (director), Joanna Amberger and Francois Schiettecatte of the OMIM project, we have divided the OMIM records into three separate tracks: OMIM Allelic Variant SNPs Variants in the OMIM database that have associated dbSNP identifiers. OMIM Genes The genomic positions of gene entries in the OMIM database. The coloring indicates the associated OMIM phenotype class. OMIM Phenotypes - Gene Unknown Regions known to be associated with a phenotype, but for which no specific gene is known to be causative. This track also includes known multi-gene syndromes. The new tracks can be found in the Phenotype and Disease Associations track group below the browser graphic and are searchable by OMIM number. In most cases, simply typing the 6-digit MIM number into the position/search box on the Browser will take you to the record. The OMIM data are the property of Johns Hopkins University and will not be available for download from UCSC. Please contact the OMIM project at omim.org for download information. UCSC thanks engineers Fan Hsu, Brooke Rhead and Robert Kuhn for this release. 9 June 2011 - UCSC Preview Browser Available Early access to ENCODE and other UCSC browser data tracks under construction is now available from the new UCSC Preview Browser site: http://genome-preview.ucsc.edu This site is a weekly mirror of our internal development server for public access. Data and tools there are under construction, have not been quality reviewed, and are subject to change at any time. We provide this site for early access, with the warning that it is less available and stable than our public site. For high-quality reviewed annotations on our production server, visit our public website: http://genome.ucsc.edu. 7 June 2011 - Updated Lizard Browser Available We have released a Genome Browser for the May 2010 genome assembly of the green anole lizard, Anolis carolinensis (Broad version AnoCar2.0, UCSC version anoCar2). This assembly, which has been sequenced to 7.1X coverage, was produced by the Broad Institute, Cambridge, MA. Bulk downloads of the sequence and annotation data are available via the Genome Browser FTP server or the Downloads page. These data have specific conditions for use. We'd like to thank the Broad Institute for providing this assembly. The lizard Genome Browser and annotation tracks were produced by Hiram Clawson, Brian Raney, and Luvina Guruvadoo. See the Credits page for a detailed list of the organizations and individuals who contributed to this release. 26 May 2011 - New Release of UCSC Genes for Mouse We've released an updated set of UCSC Genes for the mm9 (NCBI Build 37) mouse Genome Browser. This version of the gene set was generated using the same computational pipeline as the previous mm9 UCSC Genes, but is based on more recent GenBank data. The new release has 55,419 total transcripts, compared with 49,409 in the previous version. The total number of canonical genes has increased from 27,389 to 28,661. Comparing the new gene set with the previous version: 33,977 transcripts did not change between versions 69 transcripts were not carried forward to the new version 13,701 transcripts are "compatible" with those in the previous set 1,662 transcripts overlap with those in the previous set 13 May 2011 - Free Browser Training Webinar from OpenHelix The UCSC Bioinformatics Group announces two free webinars on the UCSC Genome Browser. The webinars will be conducted by OpenHelix, a provider of training on many free, publicly accessible bioinformatics and genomics resources. The webinars (one hour and 15 minutes long) will cover the topics needed to effectively use the Genome Browser. The first webinar, to be held Tuesday, May 24, 11:00-12:15 PM PDT, Introduction to the UCSC Genome Browser, is designed for new users of the UCSC Genome Browser, and those who want to improve their skills at basic navigation and display. The second webinar, UCSC Genome Browser: Custom Tracks and Table Browser, will be held Thursday, May 26, 1:00-2:15 PM PDT. Signup required. For details see Open Helix. 1 May 2011 - ENCODE User's Guide and Usability Survey The ENCODE project has just published an overview of their ongoing large-scale efforts to interpret the human genome sequence in the journal PLoS Biology. A Users Guide to the Encyclopedia of DNA Elements, highlights the scope of data production, and provides guidance for locating and using the data. With the vast amount of data now available, the ENCODE Data Coordination Center at UCSC continues to focus on improving the accessiblity and usability of this valuable resource. We invite all current and prospective users of ENCODE data to participate in the 2011 ENCODE Usability Survey. Your input will help us to make this data more accessible to the scientific community. Thank you! 18 April 2011 - dbSNP 132 Available for hg19 We are pleased to announce the release of four tracks derived from dbSNP build 132, available on the human assembly (GRCh37/hg19). dbSNP build 132 is available at NCBI. The new tracks contain additional annotation data not included in previous dbSNP tracks, with corresponding coloring and filtering options in the Genome Browser. As for prior builds of dbSNP, there is a track that contains all mappings of reference SNPs to the human assembly; it is now labeled "All SNPs (132)". Three new tracks have been added to show interesting and easily defined subsets of dbSNP: Common SNPs (132): uniquely mapped variants that appear in at least 1% of the population Flagged SNPs (132): uniquely mapped variants, excluding Common SNPs, that have been flagged by dbSNP as "clinically associated" Mult. SNPs (132): variants that have been mapped to more than one genomic location By default, only the Common SNPs (132) are visible; other tracks must be made visible using the track controls. The counts of distinct reference SNPs and their mappings to hg19 differ greatly among the tracks:
> Track | Reference SNPs | Mappings to hg19
> --- | --- | ---
> Common SNPs (132) | 13,842,381 | 14,024,295 *
> Flagged SNPs (132) | 17,899 | 18,084 *
> Mult. SNPs (132) | 1,114,599 | 3,568,988
> All SNPs (132) | 30,030,754 | 33,026,121
* The Common and Flagged tracks have more mappings than SNPs due to the alternate haplotype sequences and the pseudoautosomal regions on X and Y. SNPs are considered uniquely mapped if they map only once to a haploid reference genome. These regions add non-haploid sequence to the reference genome; therefore, multiple mappings involving these regions are still considered unique. You will find the four SNPs (132) tracks on the Human Feb. 2009 (GRCh37/hg19) browser in the "Variation and Repeats" group. Many thanks to dbSNP at NCBI for the data, and to Mary-Claire King at the University of Washington for helpful comments that motivated us to enhance our dbSNP annotations. The tracks were produced at UCSC by Angie Hinrichs, Brooke Rhead, Bob Kuhn, and Jim Kent. 18 April 2011 - Sheep Browser Released We are happy to announce a Genome Browser for the initial release of sheep (Ovis aries) genome. The Feb. 2010 Ovis aries draft assembly (NCBI project 10709, GCA_000005525.1) was produced by the International Sheep Genomics Consortium (ISGC) sequencing center. The mitochondrial genome was sequenced by Justus-Liebig-University. There are 27 chromosomes: chr1 - chr26, chrX, plus the mitochondrial sequence chrM from genbank accession NC_001941, for a total sequence length of 2,860,512,983 bases. There are 1,659,241,706 'N' bases in gaps, leaving 1,201,271,277 ACGT bases. The genome has been sequenced using 454 FLX sequencing to 3X coverage (DNA derived from six female sheep each sequenced with 0.5X coverage). Contigs were assembled based on alignment to the bovine genome and ordered into ovine chromosomes using BAC-end sequences and the virtual sheep genome. We'd like to thank the International Sheep Genomics Consortium (ISGC) sequencing center and Justus-Liebig-University for providing this assembly. We'd also like to acknowledge the UCSC team who worked on this release: Chin Li, Greg Roe, and Luvina Guruvadoo. The sheep browser annotation tracks were generated by UCSC and collaborators worldwide. 04 March 2011 - The Meaning of Red: Consensus on color scheme for CNVs Consensus was reached on color standards to represent CNV loss (red) and gain (blue) in genomics databases by DGV, NCBI, DECIPHER, UCSC and ISCA during the 1st annual ISCA Scientific Conference. At the recent ISCA Scientific Conference in Atlanta, GA, Nigel Carter, representing DECIPHER, made a plea for a standardized color scheme for representation of CNV loss (deletion) or gain (duplication). Discussions in person and by email with leaders of major CNV/genomic databases (including DGV, dbVar, ISCA, and the UCSC Genome Browser) resulted in the recommendation to utilize red to represent loss/deletion (consistent with the original convention for CGH on metaphase chromosomes) and blue to represent gain/duplication (avoiding green which is difficult for color-blind individuals to discriminate from red). Announcememnt reprinted from the website for the International Standards for Cytogenomic Arrays (ISCA) Consortium. The UCSC Genome Browser is now conforming to this standard for the DECIPHER track and the DGV track on human assemblies (which was released today) and on any future tracks derived from dbVar. Thanks to Nigel Carter, Steve Scherer, Deanna Church, Angie Hinrichs, Fan Hsu, Pauline Fujita and Robert Kuhn. 01 March 2011 - Updated Chimpanzee Browser Released We are happy to announce the release of a Genome Browser for the latest release of the chimpanzee (Pan troglodytes) genome. The Oct. 2010 assembly -- CGSC v2.1.3, UCSC version panTro3 -- was produced by the Chimpanzee Sequencing and Analysis Consortium. This assembly covers about 97 percent of the genome and is based on 6X sequence coverage. It comprises 192,898 contigs with an N50 length of 44 kb and 33,990 supercontigs with an N50 length of 8.4 Mb. Improvements introduced with the 2.1.3 assembly include the addition of over 300,000 finishing reads and the merging in of 640 finished BACS. Approximately 49,000 additional merges were made in this assembly as compared with the 2.1 assembly. The whole genome shotgun data were derived primarily from the donor Clint, a captive-born male chimpanzee from the Yerkes Primate Research Center in Atlanta, GA, USA. The sequence data were assembled and organized by the Washington University Genome Center. The underlying whole genome shotgun data were generated at the Washington University School of Medicine and the Broad Institute. For detailed information about the assembly process, see the sequencing and analysis discussion in the GenBank accession record. Bulk downloads of the sequence and annotation data are available via the Genome Browser FTP server or the Downloads page. The complete set of sequence reads is available at the NCBI trace archive. These data have specific conditions for use. We'd like to thank the International Chimpanzee Sequencing and Analysis Consortium, Washington University at St. Louis School of Medicine Genome Sequencing Center, and the Broad Institute for providing this assembly. We'd also like to acknowledge the UCSC team who worked on this release: Hiram Clawson, Greg Roe, and Donna Karolchik. The chimpanzee browser annotation tracks were generated by UCSC and collaborators worldwide. 19 January 2011 - Browser Released for Zebrafish Zv9 Assembly The most recent zebrafish assembly -- Zv9 (UCSC version danRer7, Jul. 2010) -- is now available in the UCSC Genome Browser. This assembly was produced by The Wellcome Trust Sanger Institute, UK. The Zv9 assembly comprises a sequence length of 1.4 Gb in 26 chromosomes and 1,107 scaffolds. This assembly is based on a clone path sorted with the high-density meiotic map SATMAP (Clark et al., in preparation). The data freeze was taken on 1 April 2010. The remaining gaps were filled with sequence from WGS31, a combined Illumina and capillary assembly. The assembly integration process involved sequence alignemnts as well as cDNA, marker and BAC/Fosmid end sequence placements. The zebrafish mitochondrial sequence is also available in the Genome Browser as the virtual chromosome, chrM. For more details about the Zv9 assembly, see the Sanger Institute page for the Danio rerio Sequencing Project. The danRer7 sequence and annotation data can be downloaded from the UCSC Genome Browser FTP server or downloads page. Please review the Sanger Institute guidelines for using these data. We'd like to thank the Wellcome Trust Sanger Institute for providing this assembly. The UCSC zebrafish Genome Browser was produced by Hiram Clawson, Greg Roe, Mary Goldman, Brian Raney and Donna Karolchik. See the credits page for a detailed list of the organizations and individuals who contributed to this release. 10 January 2011 - Introducing Genome Browser Right-click Navigation Several of the common display and navigation operations offered on the Genome Browser tracks page may now be quickly accessed by right-clicking on a feature on the tracks image and selecting an option from the displayed menu. Depending on context, the right-click feature will let you change the track display mode, zoom in or out to the exact position coordinates of the feature, open the "Get DNA" window at the feature's coordinates, display details about the feature, open a popup window to configure the track's display, or display the entire tracks image in a separate window for inclusion in spreadsheets or other documents. (Note that the "PDF/PS" option in the Genome Browser top navigation bar can also be used to generate a high-quality annotation tracks image suitable for printing.) To use the right-click feature, make sure the "Enable advanced javascript features" option on the tracks configuration page is checked, and configure your internet browser to allow the display of popup windows from genome.ucsc.edu. When enabled, the right-click navigation feature replaces the default contextual menu typically displayed by your internet browser when you right-click on the tracks image. A few combinations of the Mozilla Firefox browser on Mac OS do not support the right-click menu functionality using secondary click; in these instances, you must use the explicit ctrl-click action to display the menu. Credit goes to Larry Meyer and Brooke Rhead for doing the lion's share of the design, development and testing of this feature, with engineering support from Tim Dreszer and additional testing by several others on the QA team. 2 December 2010 - Searching for Tracks Just Got Easier! The number of genome assemblies and annotation tracks in the UCSC Genome Browser has increased exponentially over the past few years. Along with this growth, it has become more difficult for browser users to sort through the many tracks to find the data they're interested in. With our latest Genome Browser release, we've introduced a new track search feature that will help you to quickly and easily find and display specific annotation data sets. The search feature is available via the "track search" button on the browser gateway and tracks display pages. The default search takes one or more terms as input, and returns a list of all the browser tracks in which the name, description, group or associated metadata contains the terms. The advanced search option lets the user fine-tune the search based on the track name, description, and group. Individuals interested in the ENCODE data available on selected human genome assemblies can use the advanced search to specify particular ENCODE metadata terms, such as cell line, experiment type, etc. Once the list of search results is shown, you may choose which tracks you'd like to view in the browser, and can adjust the display modes. The search results list is sortable by multiple criteria, and provides direct links to detailed track descriptions and additional information about the tracks. Special thanks to Tim Dreszer and Larry Meyer for implementing track search, and to the QA team for their work in testing and finetuning it. We hope our users, particularly those exploring ENCODE data, will take advantage of this new feature. As always, we appreciate your feedback. Please send comments or questions to genome@soe.ucsc.edu. 24 August 2010 - New Drag and Reorder Functionality Released We are pleased to announce new functionality in the Genome Browser. It is now possible to rearrange the order that tracks appear in the browser image directly from the browser image itself. To reorder tracks, click-and-hold the side label or gray mini-button of a single track and drag the highlighted track to a new position within the image. Because reordering is now available in the browser image itself, we have removed the "enable track reordering" option from the configuration page. Thanks to Tim Dreszer and the rest of the team for implementing and testing this feature. 20 August 2010 - New ENCODE Integrated Regulation Super-track Released We are pleased to announce the release of the ENCODE Integrated Regulation super-track, a collection of regulatory tracks containing state-of-the-art information about the mechanisms that turn genes on and off at the transcription level. Individual tracks within the set show enrichment of histone modifications suggestive of enhancer and promoter activity, DNAse clusters indicating open chromatin, regions of transcription factor binding, and transcription levels. When viewed in combination, the complementary nature of the data within these tracks has the potential to greatly facilitate our understanding of regulatory DNA. The data comprising these tracks were generated from hundreds of experiments on multiple cell lines conducted by labs participating in the Encyclopedia of DNA Elements (ENCODE) project, and were submitted to the UCSC ENCODE Data Coordination Center for display on the Genome Browser. Faced with the problem of how to display such a large amount of data in a manner facilitating analysis, UCSC has developed new visualization methods that cluster and overlay the data, and then display the resulting tracks on a single screen. Each of the cell lines in a track is associated with a particular color. Light, saturated colors are used to produce the best transparent overlay. The data in the ENCODE Regulation super-track, as with all data from the production phase of the ENCODE project, have genome-wide coverage. In general, Genome Browser tracks that show ENCODE-generated data can be identified by the double-helix icon preceding the name in the track list. Currently, the ENCODE Regulation data are available only on the March 2006 (NCBI Build 36, UCSC version hg18) assembly of the human genome. For a detailed description of the datasets contained in this super-track and a discussion of how the tracks can be used synergistically to examine regions of regulatory functionality within the genome, see the track description page. 18 August 2010 - Cat Genome Browser Available We have released a Genome Browser for the latest assembly of Cat (Felis catus). The GTB V17E assembly (December 2008, UCSC version felCat4) was produced by the NHGRI Genome Technology Branch and NIH Intramural Sequencing Center, Maryland; Agencourt Bioscience Corporation, Massachusetts; NCI Laboratory of Genomic Diversity, Maryland; and Hill's Pet Nutrition, Inc, Kansas. The mitochondrial genome was sequenced by NCI Laboratory of Genomic Diversity. For detailed sequencing and assembly information, see the NCBI Felis catus assembly page. Downloads of the Cat data and annotations may be obtained from the UCSC FTP site or Downloads page. These data have been freely provided for use in the UCSC Genome Browser with specific conditions for use. Many thanks to NHGRI, Agencourt Bioscience Corporation, NCI and Hill's Pet Nutrition for providing these data. The felCat4 annotation tracks were generated by UCSC and its collaborators. We'd also like to acknowledge the UCSC Cat browser team: Chin Li, Antonio Coelho, Mary Goldman and Donna Karolchik. See the Credits page for a detailed list of the organizations and individuals who contributed to this release. 23 July 2010 - BigBed/BigWig Paper Published Last summer, we announced the release of new data formats for very large data sets: BigBed and BigWig. Read more about these data formats here. As a follow up, we are pleased to announce that we have published a paper on these new file formats. Kent WJ, Zweig AS, Barber G, Hinrichs AS, Karolchik D. BigWig and BigBed: enabling browsing of large distributed data sets. Bioinformatics. 2010 July 17. Published online in advance of print. From the abstract: BigWig and BigBed files are compressed binary indexed files containing data at several resolutions that allow the high-performance display of next-generation sequencing experiment results in the UCSC Genome Browser. The visualization is implemented using a multi-layered software approach that takes advantage of specific capabilities of web-based protocols and Linux and UNIX operating systems files, R trees, and various indexing and compression tricks. As a result, only the data needed to support the current browser view is transmitted rather than the entire file, enabling fast remote access to large distributed data sets. The supplemental materials (available online) contain the technical details about the implementation. 21 July 2010 - Free Genome Browser workshops available In the years since its introduction, the UCSC Genome Browser has become an important tool for research and teaching. As it has grown in capacity and therefore complexity, however, even experienced users sometimes have difficulty leaning how to make the most of it. We plan to provide a limited number free browser training workshops at selected institutions during the coming year. We invite you to apply. Please indicate your interest by completing our survey: Apply for free workshop 15 July 2010 - Conservation track available for zebrafish (danRer6) We are pleased to announce the release of a new Conservation track based on the zebrafish (danRer6) assembly. This track shows multiple alignments of 6 vertebrate species and measurements of evolutionary conservation using phastCons from the PHAST package. The multiple alignments were generated using multiz and other tools in the UCSC/Penn State Bioinformatics comparative genomics alignment pipeline. Conserved elements identified by phastCons are displayed in the companion "Most Conserved" track. For more details, please visit the track description page. 7 July 2010 - Happy 10th Birthday, Human Genome!
Top graph: total traffic on the UCSC domain during June-July, 2000. Bottom graph: page hit statistics on genome.ucsc.edu in the ensuing years since the Genome Browser was released.
UCSC is pleased to celebrate the 10-year anniversary of the debut of the first assembled human genome sequence and its then-fledgling visualization tool, the UCSC Genome Browser. Released on July 7, 2000, the genome sequence instantly created unprecedented web traffic on the ucsc.edu domain as researchers around the world scrambled to download the data: 0.5 terabytes per day, a record that stood for many years. David Haussler recounts that day: "Seeing the waterfall of As, Gs, Cs, and Ts pouring off our server was an emotional moment. We were witnessing the product of more than three billion years of evolution, sequences passed down from the beginning of life to present-day humans." 1 The UCSC Genome Bioinformatics group is proud of the role we have played in bringing the human genome, as well as the genomes of many other species, to the world. We'd like to thank NHGRI, HHMI, and our other funding agencies for making this service possible, and also our many users and collaborators for their suggestions, contributions, and support throughout the years. We look forward to serving as a reliable source of bioinformatics tools and genomic annotations in the years to come while facing the exciting challenges presented by rapidly advancing technology. To read more about UCSC's role in the race to assemble the first working draft of the human genome, including Jim Kent's remarkable programming feat that pulled it all together in the final weeks, see the Center for Biomolecular Science and Engineering (CBSE) website. (1) Sansom C, Morrison McKay BJ (2008) ISCB Honors David Haussler and Aviv Regev. PLoS Comput Biol 4(7): e1000101 4 June 2010 - dbSNP 131 Available for hg19 We are pleased to announce the release of dbSNP build 131, available from on the human assembly (GRCh37/hg19). The dbSNP build 131 is available at NCBI. The SNPs (131) track contains 26,033,053 mappings of 23,445,889 reference SNPs that have been mapped to the reference genome by dbSNP. This is a significant increase from the provisional hg19 mappings of build 130 (18,404,149 mappings of 17,512,501 SNPs). You will find the SNPs (131) track on the Human Feb. 2009 (GRCh37/hg19) browser in the "Variation and Repeats" group. Many thanks to dbSNP at NCBI for the data. The track was produced at UCSC by Angie Hinrichs and Mary Goldman. 3 June 2010 - Updated Marmoset Genome Browser Available We have released an updated marmoset (Callithrix jacchus) assembly, UCSC version calJac3, corresponding to the March 2009 v3.2 assembly from the Genome Center at Washington University St. Louis School of Medicine (WUSTL). This draft of the marmoset genome has approximately 6X coverage. For statistics and details on the assembly process, see the WUSTL Callithrix_jacchus-3.2 FTP server or the Downloads page. See the WUSTL Genome Center's data use policy for conditions of use. Many thanks to the Genome Center at WUSTL School of Medicine for providing the assembly data. The calJac3 annotation tracks were generated by UCSC and collaborators. See the Credits page for a detailed list of the organizations and individuals who contributed to this release. 12 May 2010 - Pig Genome Browser Released We have released a Genome Browser for the pig, Sus scrofa. This assembly (SGSC Sscrofa9.2 (NCBI project 10718, GCA_000003025.2)) was produced by the Swine Genome Sequencing Consortium and the Wellcome Trust Sanger Institute. The pig is a member of the artiodactyls (cloven-hoofed mammals), which is an evolutionary clade distinct from the primates and rodents. It is an important model for human health, particularly for understanding complex traits such as obesity and cardiovascular disease. There is extensive conserved homology with the human genome. The pig genome assembly is a hybrid of BAC end-sequencing to anchor contigs combined with whole-genome shotgun (WGS) libraries. There are 19 chromosomes: chr1 - chr18, chrX and the mitochondrial sequence chrM (GenBank accession number NC_012095) for a total sequence length of 2,262,501,571 bases. There are 31,203,023 'N' bases in gaps, leaving 2,231,298,548 ACGT bases. For more information, see the Sanger Institute's Porcine Genome Sequencing Project web page. Many thanks to the Swine Genome Sequencing Consortium and the Wellcome Trust Sanger Institute for the pig assembly data. Bulk downloads of the sequence and annotation data are available via the Genome Browser FTP server or the Downloads page. These data have specific conditions for use. The pig browser annotation tracks were generated by UCSC and collaborators worldwide. The UCSC Pig browser was produced by: Hiram Clawson, Brian Raney, Mark Diekhans, and Mary Goldman. See the Credits page for a detailed list of the organizations and individuals who contributed to this release. 6 May 2010 - UCSC Hosts Portal for Neandertal Sequence, Alignments, and Analyses In conjunction with the publication of the paper Green et al. A Draft Sequence of the Neandertal Genome in the May 7 issue of Science, the UCSC Genome Browser project has released a public Neandertal portal that may be used to access the Neandertal sequence, alignments to the UCSC hg18 (NCBI Build 36) human reference assembly and the UCSC panTro2 (Chimpanzee Sequencing and Analysis Consortium v2.1) chimpanzee reference assembly, and several associated analyses. Neandertals are the closest extinct relatives of humans. They lived in much of Europe and western Asia before disappearing from the fossil records approximately 30,000 years ago. The Neandertal genome sequence consists of short sequence fragments, usually about 50 base pairs long, mapped to the human reference genome. The sequence was derived primarily from DNA extracted from three Neandertal bones, each about 40,000 years old, found in the Vindija Cave in Croatia; smaller amounts of data were also obtained from three bones from other sites. The bulk sequencing was carried out on the Illumina GAII platform. Neandertal DNA was differentiated from the background of microbial sequences in the bone by similarity to the human or chimpanzee genomes. The draft sequence of the Neandertal genome yields important new insights into the evolution of modern humans. Among the findings discussed in the Science publication is evidence that some early modern humans, after their migration out of Africa, interbred with Neandertals, resulting in traces of Neandertal DNA sequences in the genomes of present-day non-Africans. The authors also cataloged genetic features unique to modern humans by comparing the Neandertal, human, and chimpanzee genomes. Among the genes highlighted in the study as likely to have undergone important changes in recent human evolution are those involved in cognitive development, skull structure, energy metabolism, skin morphology and physiology. We'd like to thank Richard Green (formerly of the Max-Planck Institute, and now an assistant professor of biomedical engineering at UCSC) and the many authors of the Science paper for providing the UCSC Genome Browser with these data. We'd also like to acknowledge the hard work of the UCSC Genome Browser staff who pulled together the annotations and information for the UCSC Neandertal portal: Angie Hinrichs, Katrina Learned, and Pauline Fujita. 26 Apr. 2010 - European Rabbit Genome Browser Released We have released a Genome Browser for the European rabbit, Oryctolagus cuniculus. This assembly (UCSC version oryCun2, Broad oryCun2) was produced by the Broad Institute of MIT and Harvard, Cambridge, MA. The European rabbit is the precursor of all domestic rabbits. It is a valuable model in both immunology and evolutionary biology. The genome has been sequenced to nearly 7.5X coverage. The sequence is 2.7 Gb in length and includes 21 autosomes, the X chromosome, and the mitochondrial DNA (chrM), as well as 3,219 unplaced segments. For more information on the assembly, see the Rabbit Genome Project page. Bulk downloads of the sequence and annotation data are available via the Genome Browser FTP server or the Downloads page. These data have specific conditions for use. Many thanks to the Broad Institute for the rabbit assembly data. The oryCun2 annotation tracks were generated by UCSC and collaborators. We'd also like to acknowledge the UCSC Rabbit browser team: Hiram Clawson and Antonio Coelho. See the Credits page for a detailed list of the organizations and individuals who contributed to this release. 16 Apr. 2010 - Giant Panda Genome Browser Released We have released a Genome Browser for the giant panda, Ailuropoda melanoleuca. This assembly (UCSC version ailMel1, BGI AilMel1) was produced by the Beijing Genomics Institute at Shenzhen, Shenzhen, China. The panda is a member of Ursidae, despite earlier taxonomy that marked it as a relative of the raccoon. It has become the most recognized symbol for the fight for animal conservation. This draft of the panda genome has a size of approximately 2.3 Gb at 94% coverage. The assembly comprises 81,467 scaffolds and chrM (mitochondrial DNA). For more information on the assembly, see the BGI International Giant Panda Genome Project page. Bulk downloads of the sequence and annotation data are available via the Genome Browser FTP server or the Downloads page. These data have specific conditions for use. Many thanks to the Beijing Genomics Institute at Shenzhen for the panda assembly data. The ailMel1 annotation tracks were generated by UCSC and collaborators. We'd also like to acknowledge the UCSC Panda browser team: Hiram Clawson, Ann Zweig, and Antonio Coelho. See the Credits page for a detailed list of the organizations and individuals who contributed to this release. 24 Mar. 2010 - African Savannah Elephant Genome Browser Released We have released a Genome Browser for the African savannah elephant, Loxodonta africana. This assembly (UCSC version loxAfr3, Broad loxAfr3) was produced by the Broad Institute, Cambridge, MA, USA. The elephant was the first member of Afrotheria to be sequenced. Afrotheria is the deepest node of Eutheria, and the elephant sequence should be useful in reconstructing the ancestral eutherian genome. This draft of the elephant genome has a size of approximately 3 Gb with 7X coverage. The assembly comprises 2352 scaffolds and chrM (mitochondrial DNA). For more information on the assembly, see the Broad Institute Elephant Genome Project page. Bulk downloads of the sequence and annotation data are available via the Genome Browser FTP server or the Downloads page. These data have specific conditions for use. Many thanks to the Broad Institute for the elephant assembly data. The loxAfr3 annotation tracks were generated by UCSC and collaborators. We'd also like to acknowledge the UCSC Elephant browser team: Hiram Clawson, Pauline Fujita, Vanessa Swing, Antonio Coelho, and Donna Karolchik. See the Credits page for a detailed list of the organizations and individuals who contributed to this release. 19 Mar. 2010 - California Sea Hare Genome Browser Released We have released a Genome Browser for the California sea hare, Aplysia californica. This assembly (UCSC version aplCal1, Broad version Aplcal2.0) was produced by the Broad Institute, Cambridge, MA, USA. The sea hare is the first mollusc to be sequenced, and is particularly noted for its nervous system, which is quite useful for neurobiological experimentation. This draft of the sea hare genome has a size of approximately 712 Mb with nearly 10X coverage. The assembly comprises 8766 scaffolds and chrM (mitochondrial DNA). For more information on the assembly, see the Broad Institute Aplysia Genome Project page. Bulk downloads of the sequence and annotation data are available via the Genome Browser FTP server or the Downloads page. These data have specific conditions for use. Many thanks to the Broad Institute for the sea hare assembly data. The aplcal1 annotation tracks were generated by UCSC and collaborators. We'd also like to acknowledge the UCSC Sea Hare browser team: Galt Barber, Brian Raney, Hiram Clawson, Katrina Learned, Antonio Coelho, and Donna Karolchik. See the Credits page for a detailed list of the organizations and individuals who contributed to this release. 12 Mar. 2010 - Updated Tetraodon Genome Browser Available We have released a Genome Browser for the latest assembly of Tetraodon nigroviridis. The V8 assembly (March 2007, UCSC version tetNig2) was provided by Genoscope, Evry, France, in collaboration with the Broad Institute, Cambridge, MA, USA. For detailed sequencing and assembly information, see the Genoscope Tetraodon nigroviridis assembly page. Downloads of the Tetraodon data and annotations may be obtained from the UCSC FTP site or Downloads page. These data have been freely provided by Genoscope for use in the UCSC Genome Browser with specific conditions for use. For more information about the Tetraodon nigroviridis project, see the Genoscope website. Many thanks to Genoscope and the Broad Institute for providing these data. The tetNig2 annotation tracks were generated by UCSC and its collaborators. We'd also like to acknowledge the UCSC Tetraodon browser team, which includes several new faces: Hiram Clawson, Mark Diekhans, Brian Raney, Ann Zweig, Mary Goldman, Vanessa Swing, Antonio Coelho, Robert Kuhn, and Donna Karolchik. See the credits page for a detailed list of the organizations and individuals who contributed to this release. 24 Feb. 2010 - New Gene Name Search Functionality Released UCSC has introduced a new gene search functionality in the Genome Browser, available through a "gene" text box on the gateway and annotation tracks pages. If you are searching for a particular gene, but you don't remember the exact coordinates, simply type the gene name into the box. The software will suggest gene names as you type; you can either choose a gene from the list, or finish typing your full gene name and then press "jump" or hit enter. This functionality is available now—there's nothing to configure. Start using it here. Thanks to Larry Meyer and the rest of the team for implementing and testing this feature. 25 Jan. 2010 - New Custom Track type: Binary Alignment/Map (BAM) We are pleased to announce the availability of another new track type for Custom Tracks: the Binary Alignment/Map (BAM). BAM is the compressed binary version of the Sequence Alignment/Map (SAM) format, a compact and index-able representation of nucleotide sequence alignments. Many next-generation sequencing and analysis tools work with SAM/BAM. For custom track display, the main advantage of indexed BAM over PSL and other human-readable alignment formats is that only the portions of the files needed to display a particular region are transferred to UCSC. This makes it possible to display alignments from files that are so large that the connection to UCSC would time out when attempting to upload the whole file to UCSC. Both the i BAM file and its associated index file remain on your web-accessible server (http or ftp), not on the UCSC server. UCSC temporarily caches the accessed portions of the files to speed up interactive display. 13 Jan. 2010 - Lifespan of Custom Tracks within Sessions Due to the popularity of UCSC custom tracks and sessions, we are running out of disk space for storing custom tracks accessed within sessions. Although sessions themselves are saved for one year, user-generated tracks within sessions (including custom tracks) are saved for 48 hours, the typical period for other custom tracks. Until now, because we have had space available on the server, we have attempted to keep custom tracks alive for the lifetime of the session. While we provide short-term custom track storage as a service to users who want to view their own data in the UCSC Genome Browser, we unfortunately do not have the resources to guarantee long-term data storage. Over the next few days, we will begin to actively delete custom tracks within sessions that have not been accessed within the past four months. If you actively use your custom tracks within saved sessions, they will not be deleted. Instead of uploading your data to our servers, please consider using alternate data types such as bigBed, bigWig, or other URL-based tracks that enable you to store your data locally. 11 Jan. 2010 - Zebrafish release zv8 now available in Genome Browser The most recent zebrafish assembly -- zv8 (UCSC version danRer6, Dec. 2008) -- is now available in the UCSC Genome Browser. This assembly was produced by the Wellcome Trust Sanger Institute, UK. The danRer6 assembly consists of nearly 1.5 billion bp in 11,623 scaffolds with a coverage of 6.5-7x. It includes sequence anchored to chromosomes 1-25 and chrM (mitochondrial), as well as 11,418 unplaced scaffolds. Significant problems existing in previous assemblies have been rectified in this assembly through the use of a whole-genome shotgun assembly with more coverage and a reorganization of the fingerprint contig order and orientation through more careful use of maps. For more information about this assembly, see the Sanger Institute web page for the Danio rerio Sequencing Project and the track description page for the danRer6 Assembly track. The danRer6 sequence and annotation data can be downloaded from the UCSC Genome Browser FTP server or downloads page. Please review the guidelines for using these data. We'd like to thank the Wellcome Trust Sanger Institute for providing this assembly. The UCSC zebrafish Genome Browser was produced by Galt Barber, Robert Kuhn, Katrina Learned, and Donna Karolchik. The initial set of annotation tracks was generated by the UCSC Genome Bioinformatics Group. See the credits page for a detailed list of the organizations and individuals who contributed to the release of this browser. 14 Dec. 2009 - New job posting: Biological Data Technician The UCSC Genome Browser project is looking for a bioinformatician, biologist, or software engineer with a strong biology background to collect and import data into the UCSC Genome Browser database and website. This person will work closely with external research laboratories to capture their experimental results and methods and with internal software developers and database testing staff to make the data accessible to the worldwide scientific community. Candidates must have a bachelor's degree in bioinformatics or a biological science (or equivalent experience), be proficient in UNIX/Linux command-line use, competent in UNIX shell scripting and Perl programming, and familiar with relational database concepts and SQL. Besides having the ability to quickly learn and interpret biological and technical information, the ideal candidate is an effective communicator, resourceful, and a diplomatic team player who is both quality-oriented and able to work effectively under deadline. To find more information and application instructions for this job as well as other open positions with the UCSC Genome Browser project and the UCSC Center for Biomolecular Science and Engineering, see the CBSE staff positions web page. 7 Dec. 2009 - Human Genome Browser default changing to hg19 In conjunction with the release of the UCSC Genes and Conservation tracks on the hg19 (GRCh37) human assembly, we have changed the default human browser on our website from hg18 to hg19. In general, if you are currently using the hg18 (or older) browser, the Genome Browser will continue to display that assembly for you when you start it up. However, there are circumstances in which the assembly may switch to the newer version (for instance, if you reset your browser defaults). If you find yourself in a situation where some of your favorite browser tracks have "disappeared", you may want to check that you're viewing the right assembly. 1 Dec. 2009 - New UCSC Genes and Conservation tracks released on hg19 browser We're happy to announce the release of two of our most popular data sets on the hg19/GRCh37 human Genome Browser. The UCSC Genes track is a moderately conservative set of gene predictions based on data from RefSeq, Genbank, CCDS and UniProt. The Conservation track shows multiple alignments of 46 vertebrate species and measurements of evolutionary conservation using two methods (phastCons and phyloP) from the PHAST package for all vertebrate species as well as primate and placental mammal subsets. For more information about these annotations, read the description pages that accompany these tracks. 20 Oct. 2009 - Job Opening with UCSC Genome Browser Project The UCSC Genome Browser project is currently accepting applications for a Biological Database Testing/User Support Technician (Programmer/Analyst I). We are looking for a talented self-motivated individual who would like to use their skills in computer science, biology, and bioinformatics on a fast-paced project featuring the work of top genomics scientists worldwide. For a summary of the position details and qualifications, see Biological Database Testing/User Support Technician on the Center for Biomolecular Science and Engineering (CBSE) website. For detailed job descriptions and application information, go to the UCSC Staff Employment website, click the "Search Postings" link on the sidebar, and type in job #0902365 (Testing/User Support Technician). 9 September 2009 - Changes to the bigBed/bigWig data formats If you have been taking advantage of the new bigBed format (for very large data sets), you'll be happy to hear that we have considerably slimmed down the memory footprint of the program that converts BED files into bigBed files: bedToBigBed. Because it now uses a multi-pass approach, it now takes only 1/4 the amount of RAM as the size of the uncompressed BED input file (instead of the 5x RAM it needed previously!). Read more here. Pick up the new bedToBigBed executable here. In conjunction with this change, there is also a change to the way you must specify your bigBed or bigWig custom track. When you specify the location of your local bigBed/bigWig file (on your web-accessible http, https, or ftp server), use the designation "bigDataUrl" instead of the old "dataUrl": `track type=bigBed name="My Big Bed" description="Some Data from My Lab" bigDataUrl=http://myorg.edu/mylab/myBigBed.bb` Additionally, we would like to announce a companion program to the previously-announced wigToBigWig program: bedGraphToBigWig. This program converts bedGraph files into bigWig files. The bedGraph format allows display of sparse or varying-size data. Read more here. You can download the new bedGraphToBigWig utility here. The main advantage of the bigBed and bigWig formats is that only the portions of the files needed to display a particular region are transferred to UCSC, so for large data sets, displaying bigBed/bigWig data is considerably faster than regular BED/wig data. The bigBed/bigWig file remains on your web accessible server (http, https, or ftp), not on the UCSC server. Consequently, creating your custom track is very fast. Only the portion that is needed for the chromosomal position you are currently viewing is locally cached at UCSC as a "sparse file". 10 August 2009 - Updated Yeast Genome Browser Released We have added the June 2008 release of the yeast genome (Saccharomyces cerevisiae) based on sequence from the Saccharomyces Genome Database (SGD). The sequence, open reading frame (ORF), and gene annotations were downloaded from the site ftp://genome-ftp.stanford.edu/pub/yeast/data_download. The S288C strain was used in this sequencing project. Reference information for each chromosome may be found in the SGD Systematic Sequencing Table. Bulk downloads of the sequence and annotation data are available via the Genome Browser FTP server or the Downloads page. See the Credits page for details on contributions to this release. 22 July 2009 - Updated Opossum Genome Browser Released We have released an updated opossum (Monodelphis domestica) genome browser, UCSC version monDom5, corresponding to the Broad Institute's October 2006 assembly. This draft of the opossum genome has approximately 6.8X coverage. The assembly length is nearly 3.61 billion bp including gaps (3.50 billion bp without gaps) contained on chromosomes 1-8, X, M (mitochondrial DNA), and Un (unmapped clone contigs). The N50 of the scaffolds including gaps is 60,456 kb; the N50 without gaps is 110 kb. Bulk downloads of the sequence and annotation data are available via the Genome Browser FTP server or the Downloads page. These data have specific conditions for use. Many thanks to The Broad Institute for the opossum assembly data. The monDom5 annotation tracks were generated by UCSC and collaborators worldwide. See the Credits page for a detailed list of the organizations and individuals who contributed to this release. 7 July 2009 - Engineering Job Opening with UCSC Genome Browser Project The UCSC Center for Biomolecular Science and Engineering is currently accepting applications for a full-time, experienced engineer to develop software and databases for the UCSC Genome Browser and related projects. The successful candidate must be independent, articulate, self-motivated, able to learn and integrate technical information quickly, and have a strong commitment to quality and best engineering practices. For more information about this position, see the CBSE employment page. To apply for this job, go to the UCSC Staff Employment Opportunities page, click the "Search Postings" link, and then enter job #0902109. 27 May 2009 - Australasian Genome Browser Mirror Available We are pleased to announce the availability of a public Genome Browser mirror for the Australasian research community: http://genome.qfab.org. The Queensland Facility for Advanced Bioinformatics (QFAB), in conjunction with the University of Queensland, Australia, maintains this full mirror of the UCSC Genome Browser, which is sponsored by the Australian Research Council. The QFAB mirror offers alternative access to the Genome Browser data when the UCSC site is unavailable, and may provide better performance for our Australasian users. We'd like to extend our thanks to QFAB for providing and maintaining this mirror, and in particular to Jeremy Barker and Michael Pheasant for their collaborative work with UCSC in setting up this site. 27 April 2009 - New Human Browser Released We are pleased to announce the release of the February 2009 human genome browser, UCSC version hg19. Starting with this assembly, the human genome sequence is now provided by the Genome Reference Consortium, whose goal is to correct the small number of regions in the reference that are currently misrepresented, to close as many remaining gaps as possible and to produce alternative assemblies of structurally variant loci when necessary. The hg19 browser corresponds to GRCh37. Statistics for the GRCh37 build assembly can be found on the NCBI Build 37.1 Statistics web page. The hg19 browser contains 9 haplotypes. See the Wellcome Trust Sanger Institute MHC Haplotype Project web site for additional information on the chr6 alternate haplotype assemblies. The UCSC staff responsible for producing the initial hg19 browser include Hiram Clawson, Brooke Rhead, Pauline Fujita, Ann Zweig, Katrina Learned, and Robert Kuhn. See the Credits page for a detailed list of the organizations and individuals who contributed to this release. 20 March 2009 - Two Research Scientist Positions Open The Center for Biomolecular Science & Engineering (CBSE) invites applications from outstanding PhD- or MD-level scientists for two distinct positions. Position is open until filled, but applications received after March 27 may not be considered. Cancer Genomics Director We seek an independent, creative scientist with cancer research experience to guide the group in building our cancer genomics data analysis platform into an essential tool for cancer research and an engine for personalized, genome-based cancer treatment. The successful candidate will extend our existing cancer research collaborations, conceptualize new research directions, oversee their implementation by our outstanding postdoctoral students and scientific programming staff, write papers and present results at scientific meetings, and apply for additional grants. Our exceptional collegiality and interdisciplinary collaborations make UCSC an excellent environment for an innovative scientist who can benefit from and contribute to the rapid growth in the sciences and engineering at UCSC. Read more. Medical Genomics Director We seek an independent, creative scientist who can guide the group in the direction of clinical diagnostics, pediatric/prenatal diagnostics, personalized medicine, pharmacogenomics, or related fields, building on the exceptional genome analysis resources at UCSC. The successful candidate will interface with the medical community, conceptualize genomics projects, oversee implementation by the scientific programming staff, write papers describing the projects, and apply for grants to fund future projects. Our exceptional collegiality and interdisciplinary collaborations make UCSC an excellent environment for an innovative scientist who can benefit from and contribute to the rapid growth in the sciences and engineering at UCSC. Read more. 13 March 2009 - ENCODE DCC data available We'd like to invite everyone to explore UCSC's ENCODE Data Coordination Center website, as well as the ENCODE data displayed as annotation tracks in the UCSC Genome Browser. Today's featured dataset is a track showing transcription factor binding sites determined by ChIP-seq, produced through a collaboration of Yale University, University of CA Davis, and Harvard University. Many more tracks from the Feb. 2009 and Dec. 2008 ENCODE data freezes will become available on the UCSC Genome Browser in upcoming weeks. To monitor the ENCODE data releases in the Genome Browser, see the UCSC ENCODE data release page. 17 February 2009 - Navigate with drag-and-zoom We would like to announce the release of a new navigation feature, called drag-and-zoom, in the Genome Browser. It is now possible to position your mouse over a location in the Base Position track, at the top of the browser image and define a zoom range by moving the mouse to a second place within the image. The browser will redraw at the new coordinates when the mouse button is released. 12 February 2009 - v200 code release on Darwin's 200th birthday
As coincidence would have it, we are releasing version 200 of the browser code base this week. Though we typically release code on a Friday, we couldn't resist the impulse to release a day early, on the 200th birthday of Charles Darwin, whose ground-breaking work set the stage for modern biology. 5 February 2009 - NHGRI Solicits Genome Sequencing Input The National Human Genome Research Institute (NHGRI) seeks community comments on the future of its large-scale genome sequencing program. To stimulate discussion, NHGRI has produced a white paper, "The Future of Genome Sequencing". If you'd like to review the paper or would like more information on NHGRI's long-range planning process, please visit their planning website. 30 January 2009 - 44-vertebrate Conservation Track Available We are pleased to announce the release of a new Conservation track based on the human (hg18) assembly. This track shows multiple alignments of 44 vertebrate species and measurements of evolutionary conservation using two methods (phastCons and phyloP) from the PHAST package, for all species (vertebrate) and two subsets (primate and placental mammal). The multiple alignments were generated using multiz and other tools in the UCSC/Penn State Bioinformatics comparative genomics alignment pipeline. Conserved elements identified by phastCons are also displayed in this track. For more details, visit the track description page. This track is now the default Conservation track for the hg18 human assembly. It replaces the previous 28-vertebrate Conservation track, which is now available as the "28-Way Cons" track. Many people contributed to the creation of this track including, but not limited to: Adam Siepel (Cornell University): phastCons, phyloP, and other programs in the PHAST package Webb Miller, Bob Harris and Minmei Hou (Penn State University Bioinformatics Group): blastz and multiz Hiram Clawson, Tim Dreszer, Brian Raney, Kate Rosenbloom and Ann Zweig (UCSC Genome Browser team) 3 December 2008 - Updated Horse Genome Browser Available The Sep. 2007 EquCab2 release of the horse genome (Equus caballus) is now available in the UCSC Genome Browser. This assembly, UCSC version equCab2, was produced by the Broad Institute. The horse draft genome has been sequenced to 6.8X coverage. Approximately 84% of the sequence has been anchored to chromosomes, which include autosomes 1-31 and sex chromosome X. Unanchored contigs that could not be localized to a chromosome have been concatenated into the virtual chromosome "chrUn", separated by gaps of 1,000 bp. The mitochondrial sequence is also available in the Genome Browser as the virtual chromosome "chrM". For more details about the current assembly, see the Broad Institute Horse Genome Project page. Bulk downloads of the sequence and annotation data are available from the Genome Browser FTP server or the Downloads page. These data have specific conditions for use. The UCSC Horse Genome Browser was produced by Larry Meyer, Hiram Clawson, Pauline Fujita, Brooke Rhead, and Donna Karolchik. See the Credits page for a detailed list of the organizations and individuals who contributed to this release. 7 November 2008 - Medaka Genome Browser Updated We have updated the initial UCSC Medaka Genome Browser (oryLat1) to correct an error with chrUn in which the gap relationships between the contigs within their ultracontigs were incorrect. This error was introduced by UCSC during the browser assembly process. The corrected replacement browser, oryLat2 (Oct. 2005), is based on the same v1.0 assembly produced by the National Institute of Genetics (NIG) and the University of Tokyo, Japan. We have removed the original oryLat1 assembly from the browser. 17 September 2008 - Seven Assemblies Archived: We have archived seven older assemblies of the human (hg15), mouse (mm5, mm6), rat (rn2), C. elegans (ce1), zebrafish (danRer2), and cow (bosTau1) genomes. You can continue to browse these assemblies on the Genome Browser archive server. At least two later assemblies for each of these organisms remain available on the main Genome Browser site. We do not provide blat servers or updated GenBank data for archived assemblies. However, it is still possible to lift coordinates between these assemblies and those on the main browser site. 15 September 2008 - Request for Input on ENCODE Data Release Plan The National Human Genome Research Institute (NHGRI) has updated the data release plan for the ENCODE and model organism ENCODE (modENCODE) projects. Because the plan is intended to take into account the needs and responsibilities of the resource users, NHGRI is soliciting feedback on the proposal from the research community before the plan is finalized. To facilitate this review, UCSC has made the plan available to the community here on our ENCODE website. Please send comments directly to Encode@mail.nih.gov by Wednesday, October 15, 2008. 3 September 2008 - Updated UCSC Genes Set Released for hg18 We have released an updated UCSC Genes data set on the latest human assembly (hg18, March 2006). The new annotation can be found on the hg18 Genome Browser in the "Genes and Gene Predictions" track group. The previous set of UCSC Genes on the hg18 assembly has been renamed as Old UCSC Genes in the same track group. The UCSC Genes track shows gene predictions based on data from RefSeq, Genbank, CCDS and UniProt. This is a moderately conservative set of predictions, requiring the support of one GenBank RNA sequence plus at least one additional line of evidence. The RefSeq RNAs are an exception to this, requiring no additional evidence. The track includes both protein-coding and putative non-coding transcripts. Some of these non-coding transcripts may actually code for protein, but the evidence for the associated protein is weak. Compared to RefSeq, this gene set has generally about 10% more protein-coding genes, approximately five times as many putative non-coding genes, and about twice as many splice variants. The latest version of UCSC Genes explicitly incorporates CCDS proteins in addition to the evidence included in previous versions, as well as additional data from GenBank, RefSeq, and UniProt. Although we have made every effort to preserve UCSC Gene IDs across versions, some gene IDs have changed in the new data set. In general, the ID number has been incremented if the new version of a gene is larger than the previous version, and a completely new ID has been assigned in those instances where a splice site changed or the protein-coding region shrank. However, searching on an old discontinued ID from the previous gene set will take you to the corresponding gene in the updated track. Alternatively, you can check the kg3ToKg4 table directly to find corresponding gene IDs. The UCSC Genes set was produced by Jim Kent. Thanks to Ann Zweig for heading up the testing of the new data set, and to the entire Genome Browser QA team for coordinating its release on our public site. 27 August 2008 - Zebra Finch Genome Browser Released We've added the Jul. 2008 release of the zebra finch genome (Taeniopygia guttata) to our collection of vertebrate genome browsers. The v3.2.4 draft assembly (UCSC version taeGut1) was produced by the Genome Sequencing Center at the Washington University in St. Louis (WUSTL) School of Medicine in St. Louis, MO, USA. The zebra finch genome is the second bird genome to be sequenced (following the chicken, Gallus gallus). The DNA used for the shotgun sequencing and the BAC and cosmid libraries was derived from a single male zebra finch. The initial assembly was generated using PCAP with approximately 6X coverage. About 1.0 Gb of the 1.2-Gb genome has been ordered and oriented along 33 chromosomes and one linkage group. The chromosome names are based on their homologous chromosomes in the chicken (Gallus gallus). For more assembly details, as well as a cross reference table of zebra finch and chicken chromosome names, see the WUSTL assembly notes. Bulk downloads of the sequence and annotation data are available from the Genome Browser FTP server or Downloads page. These data have specific conditions for use. Please refer to the WUSTL data use policy for additional usage guidelines and citation information. The UCSC Zebra Finch Genome Browser and initial annotations were produced by Brian Raney, Kayla Smith, Pauline Fujita, and Donna Karolchik. See the Credits page for a detailed list of the organizations and individuals who contributed to this release. 22 July 2008 - Updated C. elegans Browser Released Culminating our recent updates of the nematode browsers on our site, we've released a Genome Browser for the latest C. elegans assembly based on sequence version WS190 deposited into WormBase in May 2008. This new assembly (UCSC version ce6) was produced jointly by the Wellcome Trust Sanger Institute in Hinxton, England, and the Genome Sequencing Center at Washington University in St. Louis (WUSTL) School of Medicine, MO, USA. The ce6 browser includes a Conservation annotation and pairwise alignment tracks comparing C. elegans sequence with that of five other worms. Bulk downloads of the sequence and annotation data are available via the Genome Browser FTP server or Downloads page. Please review the WUSTL data use policy for usage restrictions and citation information. We'd like to thank WUSTL and the Sanger Institue for providing the sequence data for this assembly. The UCSC ce6 browser was produced by Hiram Clawson, Kayla Smith, Pauline Fujita, Brooke Rhead, and Donna Karolchik. See the Genome Browser Credits page for a detailed list of the organizations and individuals who contributed to this release. 26 June 2008 - New Worm Genome Available Along with the set of worm browser updates that we're currently releasing, we've added a new nematode to the collection: Caenorhabditis japonica. This genome assembly (UCSC version caeJap1, Mar. 2008) corresponds to the v. 3.0.2 assembly produced by the Genome Sequencing Center at the Washington University St. Louis (WUSTL) School of Medicine. Bulk downloads of the sequence and annotation data are available via the Genome Browser FTP server or Downloads page. Please review the WUSTL data use policy for usage restrictions and citation information. We'd like to thank WUSTL for providing the sequence data for this assembly. The UCSC caeJap1 browser was produced by Hiram Clawson, Ann Zweig, and Donna Karolchik. See the Genome Browser Credits page for a detailed list of the organizations and individuals who contributed to this release. 20 June 2008 - Two Worm Updates Released We've updated our browsers for the C. remanei and C. brenneri nematode genomes. Both sets of sequence were obtained from the Genome Sequencing Center at Washington University in St. Louis (WUSTL) School of Medicine. The C. remanei assembly (UCSC version caeRem3) corresponds to WUSTL version 15.0.1 dated May 2007. The C. brenneri assembly (UCSC version caePb2) is based on WUSTL version 6.0.1 dated Feb. 2008. Bulk downloads of the sequence and annotation data are available via the Genome Browser FTP server or Downloads page. Please review the WUSTL data use policy for usage restrictions and citation information. We'd like to thank WUSTL for providing the sequence data for these assemblies. The UCSC worm browsers were produced by Hiram Clawson, Brooke Rhead, Pauline Fujita, and Donna Karolchik. See the Genome Browser Credits page for a detailed list of the organizations and individuals who contributed to this release. 10 June 2008 - Lamprey Browser Released We have released a Genome Browser for the Mar. 2007 assembly of the lamprey genome, Petromyzon marinus. This assembly, UCSC version petMar1, was produced by the Genome Sequencing Center at the Washington University in St. Louis School of Medicine (WUSTL), St. Louis, MO, USA. Bulk downloads of the sequence and annotation data are available from the Genome Browser FTP server or Downloads page. The lamprey sequence is made freely available before scientific publication. Please see the WUSTL data use policy for usage restrictions and citation information. The UCSC Lamprey Genome Browser was produced by Hiram Clawson, Ann Zweig, Pauline Fujita, and Donna Karolchik. See the Credits page for a detailed list of the organizations and individuals who contributed to this release. 10 June 2008 - Lancelet Genome Available in Browser The Mar. 2006 release of the lancelet genome (Branchiostoma floridae) is now available in the UCSC Genome Browser. This assembly, UCSC version braFlo1, was produced by the DOE Joint Genome Institute (JGI), Walnut Creek, CA, USA. Bulk downloads of the sequence and annotation data are available from the Genome Browser FTP server or Downloads page. The lancelet sequence is made freely available before scientific publication. Please see the JGI data release policy for usage restrictions and citation information. The UCSC Lancelet Genome Browser was produced by Hiram Clawson, Ann Zweig, Pauline Fujita, and Donna Karolchik. See the Credits page for a detailed list of the organizations and individuals who contributed to this release. 5 June 2008 - Guinea Pig Browser Released The Feb. 2008 CavPor3 release of the guinea pig genome (Cavia porcellus) is now available in the UCSC Genome Browser. This assembly, UCSC version cavPor3, was produced by the Broad Institute. The guinea pig is one of 24 mammals whose genomes are being sequenced as part of the Mammalian Genome Project, funded by the National Institutes of Health. While most of these genomes are slated for low-coverage (2X), a limited subset (including the guinea pig genome) are being sequenced to a higher quality of 6-7X. The guinea pig genome has been sequenced to 6.76X coverage with 95.55% of bases assembled. A total of 3143 scaffolds cover 2,722,377,657 bases (2.17% in gaps), with 50% of the scaffolds having a (N50) length of at least 27,408,292 bases (not including gaps). For more details about the assembly, see the Broad Institute Mammmalian Genome Project page. Bulk downloads of the sequence and annotation data are available via the Genome Browser FTP server or the Downloads page. These data have specific conditions for use. The UCSC Guinea Pig Genome Browser was produced by Tim Dreszer, Kate Rosenbloom, Hiram Clawson, Kayla Smith, Robert Kuhn, and Donna Karolchik. See the Credits page for a detailed list of the organizations and individuals who contributed to this release. 5 May 2008 - GSID HIV Data Browser Now Available Global Solutions for Infectious Diseases (GSID) has announced the launch of an HIV Data Browser with clinical and viral sequence data from infected subjects in the VAX004 (North American/European) Phase III clinical trial of the AIDSVAX B/B vaccine. The browser, which is a customized version of the UCSC Genome Browser developed by the UCSC Genome Bioinformatics group and hosted by GSID, provides researchers with searchable demographic and clinical data from volunteers who became HIV infected during the VAX004 trial. Using the browser, viral sequences may be aligned with one another or with reference or consensus sequences. GSID is making these AIDSVAX data and serological samples available to the HIV research community through an agreement with VaxGen and with funding provided by the Bill and Melinda Gates Foundation. Future releases will include the addition of clinical and viral sequence data from infected subjects in the VAX003 (Thai) Phase III clinical trial of AIDSVAX B/E, and immunogenicity data from infected subjects in both the VAX004 and VAX003 trials. The browser may be expanded to include data from uninfected subjects in both trials as well. For information on accessing the GSID HIV Data Browser and background on the AIDSVAX clinical trials, visit http://www.gsid.org/index02.html. 23 Apr. 2008 - Marmoset Browser Released We'd like to announce the release of a Genome Browser and Blat server for the marmoset genome (Callithrix jacchus). The June 2007 assembly -- WUSTL version Callithrix jacchus-2.0.2, UCSC version calJac1 -- was produced by Washington University St. Louis (WUSTL) School of Medicine Genome Sequencing Center in St. Louis, MO, USA. C. jacchus, a member of the New World monkey clade, is the most widely studied marmoset. It is a popular non-human primate model due to its small body size and unique biological features, and has contributed to the study of brain function, immunity, reproductive biology and drug toxicity. C. jacchus marmosets typically give birth to twins that are somatic chimeras, i.e. each sibling is the mixture of sibling genotypes. (Excerpted from the WUSTL C. jacchus project page.) The C. jacchus genome was sequenced to 6X coverage using DNA from a female marmoset provided by the Southwestern National Primate Research Center in San Antonio, TX, USA. DNA from a full brother of the female was used as the source for the CHORI-259 BAC library. This assembly is composed of 49,724 supercontigs containing a total of approximately 3.02 billion bases. For more statistics and details on the assembly process, refer to the WUSTL Callithrix_jacchus-2.0.2 assembly page. Bulk downloads of the calJac1 sequence and annotations may be obtained from the Genome Browser FTP server or Downloads page. The sequence data can also be obtained directly from WUSTL. See the WUSTL data use policy for conditions of use. Please acknowledge WUSTL School of Medicine Genome Sequencing Center in any publications that result from the use of this sequence assembly. We'd like to thank WUSTL School of Medicine Genome Sequencing Center for providing this assembly. The initial set of marmoset browser annotation tracks were generated by UCSC. The UCSC marmoset Genome Browser team is Hiram Clawson, Robert Kuhn, Pauline Fujita, Brooke Rhead, and Donna Karolchik. See the Credits page for a detailed list of the organizations and individuals who contributed to this release. 15 Apr. 2008 - Introducing the Archaeal Genome Browser Database We'd like to introduce the Archaeal Genome Browser Database, a visualization tool and an integrated repository for archaeal functional genomics data. This resource was developed by the Lowe Lab in the UCSC Biomolecular Engineering Department, with key assistance from the UCSC Genome Browser team. The Archaeal Genome Browser Database home page can be accessed via the Archaeal Genomes menu link on the Genome Browser home page. Currently there are more than 50 completed archaeal genomes, the least studied domain of life. Although archaea and bacteria are both prokaryotes, often co-existing in the same environments, many aspects of archaeal cell biology such as DNA replication, repair, transcription, and translation are homologous to those found in eukaryotes. Some members of archaea are also notable for inhabiting extreme environments, including boiling terrestrial hot springs, black smoker vents at the bottom of the ocean, the ultra briny water of the Dead Sea, and highly acidic drainage water from ore mines, to name a few. The Archaeal Genome Browsers offer a variety of basic tracks derived from Genbank RefSeq annotation, along with published genome analyses from the Lowe Lab and external groups. The annotations include operon predictions, regulatory sequence motifs (promoters and Shine-Dalgarno), microarray data, multi-genome alignments, and protein conservation across major phylogenetic groups. The goal of the Lowe Lab is to make the Archaeal Genome Browser Database a forum for ongoing community-based genome annotation, and they welcome new experimental and bioinformatic analyses. If you would like to contribute data, or have questions or feedback about the database, contact Todd Lowe. 8 Apr. 2008 - Updated Cow Genome Browser Now Available The UCSC Genome Bioinformatics Group has released a Genome Browser and Blat server for the Oct. 2007 draft assembly of the Cow genome Bos taurus. This assembly (UCSC version bosTau4) was produced by the Baylor College of Medicine Human Genome Sequencing Center (BCM HGSC) as Baylor release Btau_4.0. The Btau_4.0 release was produced using the Atlas genome assembly system at BCM HGSC. The sequencing strategy combined BAC shotgun reads with whole genome shotgun reads from small insert libraries as well as BAC end sequences. The assembly contains chromosomes 1-29 and X as well as 11869 scaffolds (named chrUn.004.*). The mitochondrial sequence (available in the browser as "chrM") was obtained from Genbank accession GI:60101824. The Btau_4.0 assembly was tested against available bovine sequence data sets (EST sequences and finished BAC sequences) for extent of coverage (completeness). When assembled contigs were tested, over 95% of the sequences in these data sets were found to be represented, indicating that the shotgun libraries used to sequence the genome were comprehensive. Of the 1.04 million EST sequences 95.0% were contained in the assembled contigs. Assuming the ESTs are uniformly distributed throughout the genome, the estimated genome size is 2.73Gb/95% = 2.87Gb. For detailed information on the sequencing and assembly techniques, see the Baylor Bovine Genome Project web page. For a list of the chromosomes and scaffolds in this assembly, click the "Sequences" link on the cow browser gateway page. Bulk downloads of the sequence and annotation data are available via the Genome Browser FTP server or Downloads page. These data have specific conditions for use. The cow annotation tracks were generated by UCSC and collaborators worldwide. We'd like to thank Baylor College of Medicine for providing this assembly. The UCSC bosTau4 browser and documentation were produced by Hiram Clawson, Brian Raney, and Ann Zweig. See the Credits page for a detailed list of the organizations and individuals who contributed to this release. 24 Mar. 2008 - Free Genome Browser Institutional Seminars The UCSC Bioinformatics Group announces your chance to bring our hands-on computer workshop on the UCSC Genome Browser to your institution. The seminar is presented by our training partner, OpenHelix. The 3-1/2-hour introductory tutorial will cover the topics needed to effectively use our tool set, including: basic functionality of Genome Browser searching and BLAT use, Table Browser use, creating and using Custom Tracks, and an introduction to the Gene Sorter. The workshop material requires knowledge of genomic/biological concepts, but no programming skills are required. Participants will receive slide hand-outs, exercises, and UCSC Genome Browser and Table Browser Quick Reference Cards. To bring the seminar to your institution, apply on the OpenHelix website. Participating institutions are required only to: --Provide a computer classroom with internet access. The preferred number of computers is 24 or above. As an alternative to a computer room, the institution may provide a classroom with wireless access and ask participants to bring their own laptops. The seminar can be done in the morning and repeated in the afternoon to reach more users. --Conduct outreach and communication to participants as necessary. The number of seminars is limited -- apply today! Contact information: www.openhelix.com or 1-888-861-5051. About OpenHelix, LLC: OpenHelix provides the genomics knowledge you need when you need it. OpenHelix offers online self-run tutorials, web seminars, and on-site training for institutions and companies on the most powerful and popular free, web-based, publicly accessible bioinformatics resources. In addition, OpenHelix is contracted by resource providers to provide comprehensive, long-term training and outreach programs. The company has its headquarters in Seattle, with offices in San Francisco and Boston. Further information can be found at www.openhelix.com or by calling 1-888-861-5051. 10 Mar. 2008 - Orangutan Genome Browser Now Available The UCSC Genome Bioinformatics Group has released a Genome Browser and Blat server for the Jul. 2007 draft assembly of the Sumatran orangutan genome, Pongo pygmaeus abelii. This assembly (UCSC version ponAbe2, WUSTL version Pongo_albelii-2.0.2) was provided by the Genome Sequencing Center at Washington University School of Medicine in St. Louis (WUSTL), MO, USA. The orangutan genome was sequenced to 6X coverage using a female orangutan known as "Susie" from the Gladys Park Zoo (Brownsville, TX, USA). The combined sequence reads were assembled using PCAP and filtered for all known non-orangutan sequence contaminants. For more details about the assembly, see the orangutan browser gateway page and the WUSTL Pongo abelii web page. Of the 3.09 Gb of total sequence, 3.08 Gb are ordered and oriented along the chromosomes. Gap sizes between supercontigs were estimated based on their size in human, with a maximum gap size of 30 kb allowed. For a list of the chromosomes in this assembly, click the "Sequences" link on the orangutan browser gateway page. The mitochondrial sequence is also available as the virtual chromosome "chrM". Bulk downloads of the sequence and annotation data are available via the Genome Browser FTP server or Downloads page. These data have specific conditions for use. The orangutan browser annotation tracks were generated by UCSC and collaborators worldwide. We'd like to thank WUSTL for providing this assembly. The UCSC ponAbe2 browser and documentation were produced by Hiram Clawson, Kayla Smith, Robert Kuhn, Ann Zweig and Donna Karolchik. See the Credits page for a detailed list of the organizations and individuals who contributed to this release. 7 Mar. 2008 - New Reverse Functionality Released The Genome Browser team is happy to announce new functionality in the main genome browser track display. A new configuration button, "Reverse," now allows users to view the entire browser image flipped right-to-left. This is especially useful when a user's gene of interest aligns on the opposite strand from the reference assembly. Those genes then appear in the 5' to 3' direction. When the reverse function has been activated, all of the track labels usually displayed on the left side of the track (including the mini-button providing access to configuration options) are displayed on the right side. This allows users to see at a glance which direction is being displayed. All navigation options operate as expected. Thanks to Mark Diekhans, Ann Zweig, Robert Kuhn and the rest of the engineering team for implementing this feature. 8 Jan. 2008 - Additional Job Opening with UCSC Genome Browser Project In addition to the openings listed in the 12 Dec. 2007 announcement (see below), the UCSC Genome Browser project is accepting applications for Research Software Architect, a position in the UC Project Scientist academic series. For the job description, qualifications and application information, please see the Center for Biomolecular Science and Engineering website. To ensure full consideration, applications must be received by 22 Jan. 2008. 12 Dec. 2007 - Job Openings with UCSC Genome Browser Project The UCSC Genome Browser project is currently accepting applications for two positions on our development team: Software Development Engineer (Programmer/Analyst 3) and Biological Database Testing/User Support Technician (Programmer/Analyst 1). We are looking for talented self-motivated individuals who would like to use their skills in computer science, biology, and bioinformatics on a fast-paced project featuring the work of top genomics scientists worldwide. For a summary of the position details and qualifications, see the entries for Software Developer and Biological Database Testing/User Support Technician on the Center for Biomolecular Science and Engineering (CBSE) website. For detailed job descriptions and application information, go to the UCSC Staff Employment website, click the "Search Postings" link on the sidebar, and type in job #0701419 (Software Developer) or job #0701391 (Testing/User Support Technician). 15 Oct. 2007 - Genome Browser for Zebrafish Zv7 Released The latest zebrafish assembly -- Zv7 (UCSC version danRer5, July 2007) -- is now available in the UCSC Genome Browser. The Zv7 assembly was produced by The Wellcome Trust Sanger Institute in collaboration with the Max Planck Institute for Developmental Biology in Tuebingen, Germany, and the Netherlands Institute for Developmental Biology (Hubrecht Laboratory), Utrecht, The Netherlands. This assembly consists of 1,440,582,308 bp in 5,036 fragments. It includes sequence anchored to chromosomes 1-25 and chrM (mitochondrial), as well as 5010 unplaced scaffolds. The assembly was produced by integrating finished clone sequence from the physical map with whole genome shotgun assembly sequence. The N50 size is 1,153,933, n = 277 (i.e. the length such that 50% of the assembled genome lies in blocks of the N50 size or longer). For more information about this assembly, see the Sanger Institute web page for the Danio rerio Sequencing Project and the track description page for the Assembly track. The danRer5 sequence and annotation data can be downloaded from the UCSC Genome Browser FTP server or downloads page. Please review the guidelines for using these data. We'd like to thank the Wellcome Trust Sanger Institute, the Max Planck Institute for Developmental Biology, Hubrecht Laboratory and the other institutions who contributed to the sequencing and mapping effort of this release. Special thanks to the Zebrafish Genome Initiative at Children's Hospital in Boston for their collaboration on this release. The UCSC zebrafish Genome Browser was produced by Rachel Harte, Ann Zweig, and Donna Karolchik. The initial set of annotation tracks was generated by the UCSC Genome Bioinformatics Group. See the credits page for a detailed list of the organizations and individuals who contributed to the release of this browser. 10 Oct. 2007 - New Browser for Purple Sea Urchin The Sep. 2006 release of the purple sea urchin genome (Strongylocentrotus purpuratus) is now available in the UCSC Genome Browser. This assembly, UCSC version strPur2, was produced by the Baylor College of Medicine Human Genome Sequencing Center (BCM HGSC) and corresponds to their Spur_2.1 assembly. The Spur_2.1 release was assembled from BAC sequence reads (approximately 2x coverage) and whole genome shotgun reads (6x coverage), and utilizes BAC tiling path information. The BCM HGSC Atlas-2.0 genome assembly system was used to generate this assembly. The total length of all contigs greater than 1kb is 804 Mbp. When the gaps between contigs in scaffolds are included, the total span of the assembly is 907 Mbp. The estimated size of the genome based on the assembly is 814 Mbp. Compared to previous sea urchin releases, the Spur_2.1 assembly is more continuous and has fewer false duplications; contaminations identified in the previous Spur_2.0 assembly have been removed. This draft assembly may contain errors; therefore, users should exercise caution. Typical errors may include misassemblies of repeat sequences, collapses of repeat regions, and artificial duplications in polymorphic regions. However, base accuracy in contigs is usually very high with most errors near the ends of contigs. More assembly details can be found in the Spur_2.1 README file and on the BCM HGSC Sea Urchin Genome Project web page. Bulk downloads of the sequence and annotation data are available via the Genome Browser FTP server or the Downloads page. These data have specific conditions for use. The initial set of strPur2 annotation tracks was generated by UCSC. See the Credits page for a detailed list of the organizations and individuals who contributed to this release. 4 Oct. 2007 - ENCODE Genome Browser Released for hg18 Assembly The UCSC ENCODE browser for the human genome assembly hg18 (NCBI Build 36) is now available. You can access the browser directly at http://genome.ucsc.edu/ENCODE/encode.hg18.html or by clicking the ENCODE link in the sidebar menu on this page, then clicking the Regions (hg18) link in the sidebar menu on the ENCODE portal page. The hg18 ENCODE browser includes 540 data tables in 59 browser tracks that were migrated from the hg17 browser. The hg17 data coordinates were converted to hg18 coordinates using the UCSC liftOver process. To improve the accessibility of the data, related ENCODE tracks have been gathered into new configuration groupings ("super-tracks") that can be displayed or hidden using a single visiblity control. We have also reduced the number of track groups and have modified some of the group names for clarity. ENCODE tracks with whole-genome data have been moved into the standard browser track groups. For more information about the hg18 ENCODE data migration, see the News section on the UCSC ENCODE portal page and the UCSC genomeWiki. 22 Aug. 2007 - New Mouse Browser Released The latest mouse genome assembly from the Mouse Genome Sequencing Consortium, NCBI Build 37.1, is now available in the UCSC Genome Browser. This version (UCSC version mm9) is considered to be essentially finished. The Build 37.1 assembly includes approximately 2.6 Gb of sequence on chromosomes 1-19, X, Y, M (mitochondrial DNA) and Un (unmapped clone contigs). In-depth information about this assembly will become available on the NCBI website. On chromosome Y in this assembly, only the short arm has reliable mapping data; therefore, most of the contigs on the Y chromosome are unplaced. The mm9 sequence and annotation data may be downloaded from the Genome Browser FTP server or Downloads web page. The mm9 annotation tracks were generated by UCSC and collaborators worldwide. NOTE: To expedite the availability of the mm9 browser on our website, the initial release does not contain the comparative genomics annotations. These will be added to our website as they become available. Also, note that the UCSC mm9 database contains only the reference strain C57BL/6J. We'd like to thank Deanna Church and the Mouse Genome Sequencing Consortium for this assembly. We'd also like to acknowledge the work of the UCSC mm9 team: Hiram Clawson, Archana Thakkapallayil, Robert Kuhn, and Donna Karolchik. For a complete list of the individuals and organizations who participated in this assembly, see the Credits page. 22 Aug. 2007 - Latest Bovine Assembly Available The UCSC Genome Bioinformatics Group has released a Genome Browser and Blat server for the Aug. 2006 Btau_3.1 draft assembly of the cow genome. This assembly (UCSC version bosTau3) was provided by Baylor College of Medicine Human Genome Sequencing Center in Houston, TX. The Btau_3.1 release was produced by the Atlas genome assembly system at Baylor College of Medicine Human Genome Sequencing Center. The sequencing strategy combined BAC shotgun reads with whole genome shotgun reads from small insert libraries as well as BAC end sequences. The assembly contains chromosomes 1-29 and X as well as 13045 scaffolds (named chrUn.003.*). More information on the Btau_3.1 assembly can be found on the Baylor Bovine Genome Project web page and the Readme file that accompanies this release. Bulk downloads of the sequence and annotation data are available via the Genome Browser FTP server or Downloads page. Please refer to the Baylor conditions of use regarding these data. The bosTau3 annotation tracks were generated by UCSC and collaborators worldwide. We'd like to thank Baylor College of Medicine for the bovine sequence and assembly. We'd also like to acknowledge the members of the UCSC Genome Bioinformatics Group who contributed to the Cow Genome Browser: Heather Trumbower, Angie Hinrichs, Kayla Smith, and Donna Karolchik. See the Credits page for a detailed list of the organizations and individuals who contributed to this release. 2 Aug. 2007 - Five New Worm Assemblies We've updated our existing nematode browsers--for C. elegans and C. briggsae--to the latest publicly available assemblies. In addition, we've added three new worms to our collection: C. brenneri (Caenorhabditis n. sp. PB2801), C. remanei, and Pristionchus pacificus. The C. elegans sequence was obtained from WormBase; the Genome Sequencing Center at Washington University in St. Louis (WUSTL) provided sequence data for the other four assemblies.
SPECIES | UCSC VERSION | RELEASE DATE | SOURCE/RELEASE
C. elegans | ce4 | Jan. 2007 | WormBase v. WS170
C. briggsae | cb3 | Jan. 2007 | WUSTL Cb3
C. brenneri | caePb1 | Jan. 2007 | WUSTL 4.0
C. remanei | caeRem2 | Mar. 2007 | WUSTL 1.0
P. pacificus | priPac1 | Feb. 2007 | WUSTL 5.0
Bulk downloads of the sequence and annotation data are available via the Genome Browser FTP server or Downloads page. Please review the data use policy for the WUSTL-generated assemblies. We'd like to thank WUSTL, WormBase, and the Sanger Institute for providing the sequence data for these assemblies. The UCSC worm browsers were produced by Hiram Clawson, Kayla Smith, Brooke Rhead, Ann Zweig, and Donna Karolchik. See the Genome Browser Credits page for a detailed list of the organizations and individuals who contributed to this release. 13 Jul. 2007 - Drosophila melanogaster Release 5 Now Available in Genome Browser The latest D. melanogaster assembly can now be viewed in the UCSC Genome Browser. This version -- Release 5, dated Apr. 2006 (UCSC version dm3) -- was provided by the Berkeley Drosophila Genome Project (BDGP) and combines both euchromatic and heterochromatic sequence. The Release 5.1 annotations (Mar. 2007) were provided by FlyBase. The six euchromatic arms in this assembly were sequenced and assembled by BDGP from a combination of BAC and whole genome shotgun data, and have been finished to high quality. All euchromatic sequence have been compared to the restriction digest fingerprints in multiple enzymes for validity. The details of this analysis will be described in a forthcoming publication. Heterochromatic sequence from the Drosophila Heterochromatin Genome Project (DHGP) are also available in this assembly. Scaffolds that could not be unambiguously mapped to a chromosome arm have been concatenated into chrUn. chrUextra contains small scaffolds produced by the Celera shotgun assembler that could not be consistently joined with larger scaffolds. Because some of the chrUextra data are of low quality, researchers are encouraged to contact either BDGP or DHGP for further details on this resource. For more information on this assembly, see the Release 5 assembly release notes. Bulk downloads of the sequence and annotation data are available via the Genome Browser FTP server or Downloads page. We'd like to thank the BDGP, DHGP, and Flybase for providing data for this release. The dm3 Genome Browser was produced by Angie Hinrichs, Archana Thakkapallayil, Kayla Smith, and Donna Karolchik. The D. melanogaster browser annotations were generated by FlyBase, DHGP, and the UCSC Genome Bioinformatics group. See the Credits page for a detailed list of the organizations and individuals who contributed to this release. 26 Jun. 2007 - New 28-Species Conservation Track Released We are pleased to announce the release of new versions of the Conservation and Most Conserved annotation tracks for the Human March 2006 Genome Browser (hg18, NCBI Build 36). The new Conservation track displays multiple alignments of 27 vertebrate species aligned to the human genome, along with measurements of evolutionary conservation across all species in the alignment and a separate measurement of conservation across the placental mammal subset of species in the alignment. The new track includes: 5 new high-quality assemblies -- horse, platypus, lizard, and two fish (stickleback and medaka) 6 new low-coverage mammalian genomes -- bushbaby, tree shrew, guinea pig, hedgehog, common shrew, and cat 6 updated assemblies -- chimp, cow, chicken, frog, fugu, and zebrafish 10 assemblies included in the previous version of the track -- rhesus, mouse, rat, rabbit, dog, armadillo, elephant, tenrec, opossum, and tetraodon UCSC hosts browsers for the high-quality assemblies and the cat. Masked sequence data for the other genomes in the track are available from our downloads server. In addition to the expanded species list, the new Conservation track features the following improvements: additional filtering of pairwise alignments for each species to reduce paralogous alignments information about the quality of aligning species sequence included in the multiple alignment downloads new track configuration buttons to assist in selecting which species to display Bulk data downloads are available from the Genome Browser FTP server (alignments, conservation) or from the Downloads page. The previous 17-vertebrate versions of the Conservation and Most Conserved tracks remain available on the hg18 Genome Browser as the "17-Way Cons" and "17-Way Most Cons" tracks. 13 Jun. 2007 - ENCODE Findings Released to Public The findings of the ENCODE project have been released to the public today, the culmination of a four-year effort to catalog the biologically functional elements in 1 percent of the human genome. The publications, which include a group paper in the 14 June 2007 issue of Nature and 28 companion papers in the June 2007 issue of Genome Research, were authored by researchers from academic, governmental, and industry organizations located in 11 countries. The Nature issue includes a pull-out poster featuring a screenshot of the UCSC Genome Browser displaying a broad range of the ENCODE data. In the press release accompanying the publication rollout, NHGRI Director Francis S. Collins is quoted as saying "This impressive effort has uncovered many exciting surprises and blazed the way for future efforts to explore the functional landscape of the entire human genome. Because of the hard work and keen insights of the ENCODE consortium, the scientific community will need to rethink some long-held views about what genes are and what they do, as well as how the genome's functional elements have evolved. This could have significant implications for efforts to identify the DNA sequences involved in many human diseases." The main portal for the ENCODE data is the UCSC ENCODE Genome Browser. The analysis effort has been coordinated from Ensembl. Much of the primary data have been deposited in the NCBI GEO and EBI ArrayExpress databases. To access the UCSC Genome Browser ENCODE portal, click the ENCODE link in the left sidebar menu on the Genome Browser home page. For more information on the ENCODE project, including the consortium's data release and accessibility policies and a list of NHGRI-funded participants, see the NHGRI ENCODE website. To read more about UCSC's role on the project, see the news release on the UCSC Center for Biomolecular Science and Engineering website. 25 May 2007 - Platypus Assembly Available We have released a Genome Browser and Blat server for the Jan. 2007 v5.0.1 draft assembly of Ornithorhynchus anatinus (UCSC version ornAna1) produced by the Genome Sequencing Center at Washington University, St. Louis, MO (WUSTL). This assembly, which was sequenced using a combination of whole genome shotgun plasmid, fosmid and BAC end sequences, has a coverage of approximately 6X. It is comprised of about 1.84 Gb of actual sequence (excluding gap estimates), with 437 Mb anchored and ordered on chromosomes. Bulk downloads of the sequence and annotation data are available via the Genome Browser FTP server or the Downloads page. These data have specific conditions for use. We'd like to thank WUSTL for providing this assembly. The platypus Genome Browser was produced by Angie Hinrichs, Kayla Smith, Robert Kuhn, Brian Raney, and Donna Karolchik. The platypus browser annotation tracks were generated by UCSC and collaborators worldwide. See the Credits page for a detailed list of the organizations and individuals who contributed to this release. 17 May 2007 - Lizard Assembly Available in Genome Browser A Genome Browser and Blat server are now available for the Feb 2007 v1.0 draft assembly (UCSC version anoCar1) of Anolis carolinensis produced by the Broad Institute. This assembly has been sequenced to 6.8X coverage. The draft sequence contains 7,233 scaffolds comprised of nearly 1.74 Gb. Bulk downloads of the sequence and annotation data are available via the Genome Browser FTP server or the Downloads page. These data have specific conditions for use. We'd like to thank the Broad Institute for providing this assembly. The lizard Genome Browser was produced by Hiram Clawson, Archana Thakkapallayil, Robert Kuhn, and Donna Karolchik. The lizard browser annotation tracks were generated by UCSC and collaborators worldwide. See the Credits page for a detailed list of the organizations and individuals who contributed to this release. 16 May 2007 - New Dates for OpenHelix Seminars in L.A., D.C., Phila. The dates for the upcoming OpenHelix Genome Browser seminars in Washington, D.C. and Los Angeles, CA have been changed. The following updated announcement includes the new dates: The UCSC Bioinformatics Group announces three regional seminars and hands-on computer workshops on the UCSC Genome Browser presented by OpenHelix: Philadelphia -- Wednesday, 13 June Washington. D.C./Baltimore -- Wednesday, 20 June Los Angeles -- Wednesday, 27 June All sessions will be held 1 p.m. to 4 p.m. These introductory sessions are geared towards anyone with a basic knowledge of genomic and biological concepts who is interested in learning how to use the UCSC Genome Browser. No programming experience is required. The seminars will cover the topics necessary to learn how to effectively use the browser tool set, including basic Genome Browser functionality, searching and BLAT use, Table Browser use, creating and using custom annotation tracks, and an introduction to the Gene Sorter. Lectures will be accompanied by hands-on computer exercises conducted directly on the Genome Browser web site. Participants receive a complete set of slide and exercise handouts and printed Quick Reference Cards. For further information or to make a reservation, visit the OpenHelix website or call 1-888-861-5051. Register early; seating is limited. Academic and student discounts are available. 14 May 2007 - Horse Genome Browser Now Available The Jan. 2007 EquCab1 release of the horse genome (Equus caballus) is now available in the UCSC Genome Browser. This assembly, UCSC version equCab1, was produced by the Broad Institute. The horse draft genome has been sequenced to 6.8X coverage. Approximately 84% of the sequence has been anchored to chromosomes, which include autosomes 1-31 and sex chromosome X. Unanchored contigs that could not be localized to a chromosome have been concatenated into the virtual chromosome "chrUn", separated by gaps of 1,000 bp. The mitochondrial sequence is also available in the Genome Browser as the virtual chromosome "chrM". For more details about the assembly, see the Broad Institute Horse Genome Project page. Bulk downloads of the sequence and annotation data are available via the Genome Browser FTP server or the Downloads page. These data have specific conditions for use. The UCSC Horse Genome Browser was produced by Fan Hsu, Brooke Rhead, Robert Kuhn, Hiram Clawson, Angie Hinrichs, Kate Rosenbloom, and Donna Karolchik. See the Credits page for a detailed list of the organizations and individuals who contributed to this release. 27 April 2007 - Medaka Genome Browser Released We're happy to announce the release of a Genome Browser and Blat server for the Medaka Version 1.0 draft assembly (Apr. 2006, UCSC version oryLat1). This assembly was produced in Japan by the National Institute of Genetics (NIG) and the University of Tokyo. It is equivalent to Ensembl's Oct. 2005 MEDAKA1 data set. The v1.0 assembly has been sequenced to 10.6X coverage. It consists of approximately 700.4 million bp (excluding gaps) on chromosomes 1-24. 7,299 scaffolds comprised of nearly 36,500 contigs of unplaced sequence are displayed on the virtual chromosome "chrUn". These contigs are spaced with a 10 bp gap; scaffold gaps are 100 bp in size. The medaka mitochondrial sequence is also available in the Genome Browser as the virtual chromosome "chrM". Bulk downloads of the sequence and annotation data are available via the Genome Browser FTP server or the Downloads page. See the University of Tokyo medaka website for the data release policy for this assembly. The Medaka browser annotation tracks were generated by UCSC and collaborators worldwide. See the Genome Browser Credits page for a detailed list of the organizations and individuals who contributed to this release. 18 April 2007 - Free Genome Browser Seminar at Experimental Biology 2007 OpenHelix will present a free introductory seminar on the Genome Browser during Experimental Biology 2007, April 29-May 1, in Washington, D.C. The tutorial will cover the topics needed to effectively use the Genome Browser, including: basic functionality of Genome Browser searching and BLAT use, Table Browser use, creating and using Custom Tracks, and an introduction to the Gene Sorter. The seminar will be held on Monday April 30, 4:30-5:30p.m. in Room 204C in the Washington, D.C. Convention Center. It is open to any interested conference attendee with a basic knowledge of genomic/biological concepts; no programming skills are needed. The tutorial requires no advanced registration or fee. Attendees will receive a free download of the training materials. For more information, see the OpenHelix website or call 1-888-861-5051. In addition to the tutorial, OpenHelix will be presenting brief introductory overviews of the UCSC Genome Browser and other bioinformatics resources during show hours at Booth 330/332. Stop by the booth for more information and to receive your free Genome Browser Quick Reference Cards. 11 April 2007 - Latest Fugu Assembly Available in Genome Browser The UCSC Genome Browser now includes the latest release of the Fugu genome. The v4.0 whole genome shotgun assembly (Oct. 2004, UCSC fr2) was provided by the US DOE Joint Genome Institute (JGI) as part of the International Fugu Genome Consortium led by the JGI and the Singapore Institute of Molecular and Cell Biology (IMCB). This version has been sequenced to approximately 8.5X coverage. The assembly contains 7,213 scaffolds covering 393,312,790 bp. The UCSC browser displays the scaffolds on the virtual chromosome chrUn with gaps of 1,000 bp between scaffolds. The scaffolds range in size from 2,223 bp to 7,245,445 bp. Fifty percent of the sequence (196,648,171 bp) is contained within 125 scaffolds of size 858,115 or greater (N50). The Fugu mitochondrial sequence is also available as the virtual chromosome chrM (GenBank accession: NC_004299.1). Bulk downloads of the sequence and annotation data are available via the Genome Browser FTP server or Downloads page. These data have been freely provided by the JGI for use in the UCSC Genome Browser. Many thanks to the JGI, IMCB, and the International Fugu Genome Consortium for the assembly data. The UCSC Fugu Genome Browser was produced by Cory McClean, Hiram Clawson, Ann Zweig, and Donna Karolchik. The annotation tracks were generated by UCSC and collaborators worldwide. See the Credits page for a detailed list of the organizations and individuals who contributed to this release. 6 April 2007 - New UCSC Gene Prediction Set Released We are pleased to announce the release of a new gene prediction set, UCSC Genes, on the latest human Genome Browser (hg18, NCBI Build 36). This annotation, which includes putative non-coding genes as well as protein-coding genes and 99.9% of RefSeq genes, is the next generation of the Known Genes set that UCSC has been providing for several years and supersedes the existing Known Genes annotation on the hg18 assembly. The UCSC Genes is a moderately conservative prediction set based on data from RefSeq, GenBank, and UniProt. Each entry requires the support of one GenBank RNA sequence plus at least one additional line of evidence, with the exception of RefSeq RNAs, which require no additional evidence. Some of the non-coding transcripts in the set may actually code for protein, but the evidence for the associated protein is weak at best. Compared to RefSeq, this gene set generally has about 10% more protein-coding genes, approximately five times as many putative non-coding genes, and about twice as many splice variants. A new companion track to UCSC Genes, Alt Events, shows various types of alternative splicing, alternative promoter, and other events that result in more than a single transcript from the same gene. This track is based on an analysis by the txgAnalyse program of splicing graphs produced by the txGraph program. The UCSC Genes set is produced using a computational pipeline developed at UCSC by Jim Kent, Chuck Sugnet and Mark Diekhans. The programs used to construct the Alt Events data set were written by Jim Kent. For detailed information about the process used to construct the genes set, see the track description page. In upcoming months, we plan to release UCSC Genes sets on several organisms in addition to human. The UCSC Genes annotations will be updated approximately every three months. As part of this change, we are now using our own UCSC Genes accession numbers as the primary key into the underlying knownGene table, rather than the GenBank mRNA accessions we used in the previous Known Genes prediction set. Note that this may affect external sites with URLs that link into our genes track using the older-style accessions. We will continue to provide the older Known Genes track on hg18 under the name "Old Known Genes". You may find the following tables useful in referencing the older gene set and converting between the two sets: knownGeneOld2: new name for table underlying the old Known Genes (previously called knownGene) kgXrefOld2: new name for table that contains data for converting old Known Genes IDs to other IDs (previously called kgXref) kg2ToKg3: data for converting old Known Genes IDs to the newer UCSC Genes IDs We'd like to acknowledge the many people affiliated with the UCSC Genome Bioinformatics group who worked hard to release this new annotation: developers Jim Kent, Mark Diekhans, and Fan Hsu (with technical support from several other engineers in the group); David Haussler; our splendid QA team -- Archana Thakkapallayil, Ann Zweig, Robert Kuhn, Kayla Smith, and Brooke Rhead; our build engineer -- Andy Pohl; and our sysadmin group. We'd also like to thank Chuck Sugnet for his input, the people and organizations maintaining the RefSeq, UniProt, and GenBank databases, and the scientists worldwide who have contributed to them. If you have any questions about this new release, feel free to contact us at genome@soe.ucsc.edu (general questions) or genome-mirror@soe.ucsc.edu (mirror-specific questions). 27 March 2007 - Stickleback Assembly Released in Genome Browser We have released a Genome Browser and Blat server for the Feb. 2006 v1.0 draft assembly of Gasterosteus aculeatus produced by the Broad Institute. This assembly has been sequenced to approximately 6X coverage. An estimated 87% of the sequence has been anchored to chromosomes (chrI - chrXXI). Of the remaining unanchored scaffolds, those that could be localized to a chromosome have been concatenated into the virtual chromosome "chrUn" with 1000bp gaps between scaffolds. The stickleback mitochondrial sequence is also available as the virtual chromosome "chrM". Bulk downloads of the sequence and annotation data are available via the Genome Browser FTP server or the Downloads page. These data have specific conditions for use. The stickleback browser annotation tracks were generated by UCSC and collaborators worldwide. See the Credits page for a detailed list of the organizations and individuals who contributed to this release. 16 February 2007 - New Browser Session-Sharing Function Available We are pleased to announce the release of a new session management functionality in the Genome Browser, which allows users to save and share browser sessions. Users are now able to configure their browsers with specific track combinations, including custom tracks, and save the configuraton options. Multiple sessions may be saved for future reference, for comparison of scenarios or for sharing with colleagues. Saved sessions persist for one year after the last access, unless deleted. Custom tracks persist for at least 48 hours after the last time they are viewed. The new feature may be accessed via the "Sessions" link in the top blue bar in any assembly. To ensure privacy and security, users must login to the genomewiki site and create a username and password. Individual sessions may be designated by the user as either "shared" or "non-shared" to protect the privacy of confidential data. To avoid having a new shared session from someone else override existing Genome Browser settings, users are encouraged to open a new web-browser instance or to save existing settings in a session before loading a new shared session. The Sessions feature was written by Angie Hinrichs of the UCSC Genome Bioinformatics Group and released with the assistance of Kayla Smith and Robert Kuhn. 2 February 2007 - New Genome Graphs Tool Available in Genome Browser We are pleased to announce the release of a new software tool in the Genome Browser collection, the Genome Graphs tool. Genome Graphs offers the ability to upload and display genome-wide data sets such as the results of genome-wide SNP association studies, linkage studies and homozygosity mapping. The Genome Graphs tool may be accessed from the menu on the UCSC Genome Bioinformatics home page. The initial release of Genome Graphs includes the following features: upload several sets of genome-wide data and display them simultaneously click on an area of interest and go directly to the genome browser at that position set a significance threshold for your data and view only regions that meet that threshold view the genes that exist in areas where your data meet your significance threshold For more information about the Genome Graphs tool, visit the Gateway page or consult the Getting Started on Genome Graphs section in the User's Guide. Genome Graphs was written by Jim Kent of the UCSC Genome Bioinformatics Group and released with the assistance of Ann Zweig. 22 January 2007 - Cat Assembly Available in Genome Browser The Mar. 2006 release of Felis catus (UCSC version felCat3) is now available in the Genome Browser. This assembly was produced by The Broad Institute of MIT/Harvard and Agencourt Bioscience. The felCat3 genome has been sequenced to 2X coverage and consists of 217,790 scaffolds. The total contig length for this assembly is approximately 1.6 Gb spanning nearly 4.0 Gb (with 60.1% in gaps). There are 749,376 contigs, with an N50 length of 2,506 bases. There are 149,283 supercontigs, with an N50 length of 49,769 bases (not including gaps). The N50 size is the length such that 50% of the assembled genome lies in blocks of the N50 size or longer. The felCat3 sequence and annotation data can be downloaded from the Genome Browser FTP server or Downloads page. Please review the guidelines for using the cat assembly data. Many thanks to The Broad Institute for providing these data. The UCSC cat Genome Browser was produced by Heather Trumbower, Angie Hinrichs, Mark Diekhans, Brooke Rhead, and Archana Thakkapallayil. The initial set of annotation tracks was generated by the UCSC Genome Bioinformatics Group. See the Genome Browser Credits page for a detailed list of the organizations and individuals who contributed to the release of this browser. 1 January 2007 - Upcoming Genome Browser Seminars: SF, Seattle, NYC, Cleveland The UCSC Bioinformatics Group announces four regional seminars and hands-on computer workshops on the UCSC Genome Browser, presented by OpenHelix: San Francisco, CA -- Wednesday, 31 January Seattle, WA -- Thursday, 1 February New York City, NY -- Tuesday, 13 February Cleveland, OH -- Wednesday, 14 February Two sessions will be offered for the New York and Cleveland seminars: 9:00 a.m. to noon and 1 p.m. to 4 p.m. Only the afternoon session will be offered in San Francisco and Seattle. These introductory sessions are geared towards anyone with a basic knowledge of genomic and biological concepts who is interested in learning how to use the UCSC Genome Browser. No programming experience is required. The seminars will cover the topics necessary to learn how to effectively use the browser tool set, including basic Genome Browser functionality, searching and BLAT use, Table Browser use, creating and using custom annotation tracks, and an introduction to the Gene Sorter. Lectures will be accompanied by hands-on computer exercises conducted directly on the Genome Browser web site. Participants receive a complete set of slide and exercise handouts and printed Quick Reference Cards. For further information or to make a reservation, visit the OpenHelix website or call 1-888-861-5051. Register early; seating is limited. Academic and student discounts are available. 13 November 2006 - UCSC Genome Browser Wiki The UCSC Genome Bioinformatics group has launched a wiki site for sharing information about the UCSC Genome Browser and its data. The wiki -- at http://genomewiki.ucsc.edu -- provides an informal forum for our browser users, mirror sites, and staff to discuss topics of interest in the genome biology field and exchange usage tips, scripts/programs, and notes about mirroring the Genome Browser and working with the Genome Browser source. As with most wiki pages, general users are welcome to edit and add pages (login required). Please note that all content created on the genomewiki site becomes a public resource; content persists in the history of a page even after it has been deleted. 24 October 2006 - Free Genome Browser Training Sessions at AHA Scientific Sessions OpenHelix will present a free seminar on the UCSC Genome Browser at the American Heart Association's Scientific Sessions 2006 in Chicago, IL, on 12 Nov. from 7:00 - 8:30 p.m. The seminar will be held in the Hyatt Regency Conference Center, Room CC21, 2233 South Martin Luther King Drive, Chicago, IL. The introductory tutorial will cover the topics needed to effectively use the Genome Browser including: basic functionality of Genome Browser searching and BLAT use, Table Browser use, creating and using Custom Tracks, and an introduction to the Gene Sorter. The jointly-sponsored seminar will also include an introduction to VISTA comparative genomics tools. The session is open to anyone attending the AHA Scientific Sessions; no registration or fee is required. Participants should have a basic knowledge of genomic/biological concepts, but no programming skills are needed. Attendees will receive a free download of training materials, and refreshments will be served. This event is not part of the official Scientific Sessions 2006 as planned by the AHA Committee on Scientific Sessions Program. OpenHelix will also be presenting brief introductory overviews of the Genome Browser and other resources during show hours at booth 2464. Stop by the booth for more information and to receive your free Quick Reference Cards for the Genome Browser and Table Browser. 6 October 2006 - Announcing Upgrades to the Genome Browser Custom Tracks Functionality We have enhanced one of the popular tools in the Genome Browser collection: the custom tracks utility. The new custom tracks tool provides a more user-friendly interface and increased flexibility for creating and managing your custom tracks. The initial release of this upgraded tool includes the following features: Add and display multiple custom tracks simultaneously via URL, file or text Add to, delete and modify the uploaded custom tracks set using a new track management interface Load and manage custom tracks from multiple assemblies Create and upload description pages for custom tracks Custom tracks will now persist on our server for 48 hours after last access (rather than 8 hours) For more information about the new custom tracks functionality, see the Genome Browser Users's Guide. The hgCustom CGI was written by Kate Rosenbloom with the assistance of Archana Thakkapallayil, Ann Zweig and other members of the UCSC Genome Bioinformatics Group. 7 September 2006 - Old Rhesus Assembly Archived The Jan. 2005 rheMac1 draft assembly has been moved from the main Genome Browser website to our archive server. The data remain available for browsing and downloading, although blat services are no longer supported. 8 August 2006 - New Opossum Assembly Available in Genome Browser The UCSC Genome Browser now includes the latest draft assembly of the opossum genome. The Jan. 2006 release of Monodelphis domestica (UCSC version monDom4) was sequenced and assembled by The Broad Institute, Cambridge, MA, USA. This draft, which has approximately 6.5X coverage, has an assembly length of nearly 3.61 billion bp including gaps (3.50 billion bp without gaps) contained on chromosomes 1-8, X, and Un. The N50 of the genome including gaps is 104,359 bp; the N50 without gaps is 107,990. The N50 size is the length such that 50% of the assembled genome lies in blocks of the N50 size or longer. The monDom4 sequence and annotation data can be downloaded from the Genome Browser FTP server or Downloads page. Please review the guidelines for using the opposum assembly data. Many thanks to The Broad Institute for providing these data. The UCSC opossum Genome Browser was produced by Hiram Clawson, Archana Thakkapallayil, Ann Zweig, Kayla Smith and Donna Karolchik. The initial set of annotation tracks was generated by the UCSC Genome Bioinformatics Group. See the Genome Browser Credits page for a detailed list of the organizations and individuals who contributed to the release of this browser. 1 August 2006 - v2.1 Chicken Assembly Available in Genome Browser We have updated the Chicken Genome Browser to include the May 2006 v2.1 assembly (UCSC version galGal3) produced by the Genome Sequencing Center at the Washington University School of Medicine in St. Louis, MO, USA (WUSTL). The source of this sequence was a female inbred Red Jungle Fowl (Gallus gallus), the ancestor of domestic chickens. The chicken genome is the first of the avian genomes to be sequenced. In this assembly, 198,000 additional reads covering all contig ends and regions of low quality have been added to the original assembly's 6.6X coverage. Approximately 95% of the sequence has been anchored to chromosomes, which include autosomes 1-24, 26-28, and 32, and sex chromosomes W and Z. (In contrast to mammals, the female chicken is heterogametic (ZW) and the male is homogametic (ZZ).) The remaining unanchored contigs that could be localized to a chromosome have been concatenated into the virtual chromosomes "chr*_random", separated by gaps of 10,000 bp. Unanchored contigs that could not be localized to a chromosome have been concatenated into the virtual chromosome "chrUn_random", separated by gaps of 100 bp to reduce the total size of chrUn_random. The chicken mitochondrial sequence is also available as the virtual chromosome "chrM". Although centromere positions are indicated on this assembly, little is known of their exact sequence. The centromeres of 18 chromosomes were tentatively localized based on FISH hybridization using BAC clones, genetic markers flanking the centromeres in coordination with mapping gaps in the physical map, repetitive sequence content, and analysis of proximity to the constrictions of the mitotic metaphase chromosomes. For more information on the process used to create the chromosomal sequences and assign centromere locations, see the WUSTL Gallus gallus assembly release notes. Bulk downloads of the chicken sequence and annotations may be obtained from the Genome Browser FTP server or Downloads page. These data have specific conditions for use. We'd like to thank WUSTL, who provided the sequence, physical map, assembly, and assembly/map for this release. The genetic mapping and linkage analysis were produced through a collaborative effort of labs in The Chicken Mapping Consortium. The chicken browser annotation tracks were generated by UCSC and collaborators worldwide. See the Credits page for a detailed list of acknowledgements. The UCSC Chicken Genome Browser was produced by Angie Hinrichs, Kayla Smith, and Donna Karolchik. 20 July 2006 - New Chimpanzee Genome Browser Released We are happy to announce the release of a Genome Browser for the latest release of the chimpanzee (Pan troglodytes) genome. The Mar. 2006 assembly -- labeled Chimp Build 2 Version 1 (UCSC version panTro2) -- was produced by the Chimpanzee Sequencing and Analysis Consortium. This 6X whole genome assembly contains sequence from the initial 4X chimpanzee assembly described and analyzed in Nature (The Chimpanzee Sequencing and Analysis Consortium, 2005), with additional 2X sequence generated, assembled, and assigned to chromosomes by the Genome Sequencing Center of Washington University School of Medicine, St. Louis, MO, USA. The whole genome shotgun data were derived primarily from the donor Clint, a captive-born male chimpanzee from the Yerkes Primate Research Center in Atlanta, GA, USA. The reads were assembled using the whole-genome assembly program PCAP. For information about the assembly process, see the panTro2 Gateway page. This assembly covers about 97 percent of the genome and is based on 6X sequence coverage. It is composed of 265,882 contigs with an N50 length of 29 kb and 44,460 supercontigs with an N50 length of 9.7 Mb. The total contig length, not including estimated gap sizes, is 2.97 Gb. Of that total, 2.82 Gb of sequence have been ordered and oriented along specific chimpanzee chromosomes, 107 Mb have been placed in chr*_random, and 50 Mb remain in chrUn. A major difference between this assembly and the previous Nov. 2003 version is the chromosomal numbering scheme, which has been changed to reflect a new standard that preserves orthology with human chromomes. Proposed by E.H. McConkey in 2004, the new numbering convention was subsequently endorsed by the International Chimpanzee Sequencing and Analysis Consortium. This standard assigns the identifiers "2a" and "2b" to the two chimp chromosomes that fused in the human genome to form chromosome 2. Note that the genome assembly shown in the Nov. 2003 panTro1 Genome Browser retains the older numbering scheme, in which these chromosomes are numbered 12 and 13. Bulk downloads of the sequence and annotation data are available via the Genome Browser FTP server or the Downloads page. The complete set of sequence reads is available at the NCBI trace archive. These data have specific conditions for use. We'd like to thank the International Chimpanzee Sequencing and Analysis Consortium, Washington University at St. Louis School of Medicine Genome Sequencing Center, and the Broad Institute for providing this sequence. We'd also like to acknowledge the UCSC team who worked on this release: Kate Rosenbloom, Brian Raney, Hiram Clawson, Ann Zweig, Archana Thakkapallayil, and Donna Karolchik. The chimpanzee browser annotation tracks were generated by UCSC and collaborators worldwide. 20 June 2006 - Genome Browser Released for Baylor v3.4 Rat Assembly The UCSC Genome Bioinformatics group has released a Genome Browser for the v3.4 rat (Rattus norvegicus) genome. This assembly--UCSC version rn4, November 2004--was produced by the Atlas group at Baylor Human Genome Sequencing Center (HGSC) as part of the Rat Genome Sequencing Consortium. The sequence was assembled using a hybrid approach that combines the clone-by-clone and whole genome shotgun methods. The assembly is a minor update to version 3.3 that spliced in 54.6 Mb finished BAC sequences; the overall statistics are unchanged from releases 3.0 to 3.4. The 3.x assemblies reflect several sequence additions and software improvements over the previous 2.x assemblies, including the sequencing of over 1100 new BACs to cover gaps, an improved marker set from the Medical College of Wisconsin, a new FPC map from the BC Cancer Agency Genome Sciences Centre, and improved linking of bactigs. For detailed information and statistics about the 3.x assemblies, see the Baylor HGSC Rat Genome Project web page. Bulk downloads of the sequence and annotation data are available via the Genome Browser FTP server or the Downloads page. These data are made available with specific conditions for use. We'd like to thank the Rat Genome Sequencing Consortium and the Baylor HGSC for providing this assembly. We'd also like to acknowledge the UCSC team who produced the rn4 Genome Browser: Angie Hinrichs, Fan Hsu, Brooke Rhead, Archana Thakkapallayil, Kayla Smith, Ann Zweig, Robert Kuhn, and Donna Karolchik. The rn4 annotation tracks were generated by UCSC and collaborators worldwide. See the Credits page for a detailed list of the organizations and individuals who contributed to this release. 12 June 2006 - Latest X. tropicalis Assembly Available in Browser The v.4.1 Xenopus tropicalis assembly is now available on the UCSC Genome Browser. This whole genome shotgun assembly (xenTro2, August 2005) was generated by the U.S. DOE Joint Genome Institute (JGI) using the Jazz assembler. It contains 19,501 scaffolds with an average coverage of 7.65X. Roughly half the genome is contained in 272 scaffolds, each of at least 1.56 Mb in length. In this release, some scaffolds showing homology to a known prokaryotic contaminant as well as non-cellular or vector contamination have been removed by the JGI and placed in a separate directory. The X. tropicalis assembly will be improved over the coming year by additional sequencing of large insert clones, targeted gap closure, and the incorporation of physical and genetic mapping information as it becomes available. For more information about the 4.1 assembly, see the JGI X. tropicalis website. The xenTro2 sequence and annotation data can be downloaded from the UCSC Genome Browser FTP server or downloads page. These data have specific conditions for use. Many thanks to the JGI and the other institutions who contributed to the sequencing and mapping effort for this release. The xenTro2 Genome Browser was produced by Angie Hinrichs, Kayla Smith, Robert Kuhn, and Donna Karolchik. The xenTro2 annotation tracks were generated by UCSC and collaborators worldwide. See the credits page for a detailed list of the organizations and individuals who contributed to this release. 25 May 2006 - Zv6 Zebrafish Browser Released The latest zebrafish assembly -- Zv6 (UCSC version danRer4, March 2006) -- is now available in the UCSC Genome Browser. The Zv6 assembly was produced by The Wellcome Trust Sanger Institute in collaboration with the Max Planck Institute for Developmental Biology in Tuebingen, Germany, and the Netherlands Institute for Developmental Biology (Hubrecht Laboratory), Utrecht, The Netherlands. This assembly consists of 1,626,077,335 bp in 6.653 scaffolds (N50 = 1,247,221 bp) with a sequence coverage of approximately 6.5-7x. The sequence has been anchored to chromosomes 1-25, chrM (mitochondrial), chrNA_random, and chrUn_random. For more information about this assembly, see the Sanger Institute web page for the Danio rerio Sequencing Project. The danRer4 sequence and annotation data can be downloaded from the UCSC Genome Browser FTP server or downloads page. Please review the guidelines for using these data. We'd like to thank the Wellcome Trust Sanger Institute, the Max Planck Institute for Developmental Biology, Hubrecht Laboratory and the other institutions who contributed to the sequencing and mapping effort of this release. Special thanks to the Zebrafish Genome Initiative at Children's Hospital in Boston for their collaboration on this release. The UCSC zebrafish Genome Browser was produced by Rachel Harte, Archana Thakkapallayil, Robert Kuhn, Ann Zweig, and Donna Karolchik. The initial set of annotation tracks was generated by the UCSC Genome Bioinformatics Group. See the credits page for a detailed list of the organizations and individuals who contributed to the release of this browser. 10 May 2006 - NCBI Mouse Build 36 Released in Genome Browser The latest mouse genome assembly from the Mouse Genome Sequencing Consortium, NCBI Build 36, is now available in the UCSC Genome Browser. This version (UCSC version mm8) is considered to be essentially finished. The Build 36 assembly includes approximately 2.6 Gb of sequence on chromosomes 1-19, X, Y, M (mitochondrial DNA) and Un (unmapped clone contigs). For in-depth information about the process used to assemble this version, see the NCBI website. On chromosome Y in this assembly, only the short arm has reliable mapping data; therefore, most of the contigs on the Y chromosome are unplaced. Note that the UCSC mm8 database contains only the reference strain C57BL/6J. The mm8 sequence and annotation data may be downloaded from the Genome Browser FTP server or Downloads web page. The mm8 annotation tracks were generated by UCSC and collaborators worldwide. We'd like to thank Deanna Church and the Mouse Genome Sequencing Consortium for this assembly. We'd also like to acknowledge the work of the UCSC mm8 team: Hiram Clawson, Fan Hsu, Kayla Smith, Ann Zweig, Robert Kuhn, Brooke Rhead, Archana Thakkapallayil, and Donna Karolchik. For a complete list of the individuals and organizations who participated in this assembly, see the Credits page. 14 April 2006 - NCBI Build 36.1 Human Reference Sequence Available in Browser The latest human genome reference sequence assembly (NCBI Build 36.1, March 2006) is now available as database hg18 in the UCSC Genome Browser. This sequence, which was obtained from NCBI, was produced by the International Human Genome Sequencing Consortium. The hg18 assembly contains four alternate haplotype regions: chr22_h2_hap1 -- an alternate chromosome 22 assembly that contains the CYP2D6 gene (NT_113959.1). CYP2D6 is deleted in the reference assembly. chr5_h2_hap1 -- a chromosome 5 alternate assembly of the SMN1 gene region (NT_113801.1, NT_113802.1). chr6_cox_hap1 -- an A1-B8-DR3 alternate haplotype assembly of the chromosome 6 MHC region based on sequence data from the COX library (NT_113891.1). chr6_qbl_hap2 -- an A26-B18-DR3 alternate haplotype assembly of the chromosome 6 MHC region based on sequence data from the QBL library (NT_113892.1, NT_113893.1, NT_113894.1, NT_113895.1, NT_113896.1, NT_113897.1). See the Wellcome Trust Sanger Institute MHC Haplotype Project web site for additional information on the chr6 alternate haplotype assemblies. The Y chromosome in this assembly contains two pseudoautosomal regions (PARs) at chrY:1-2709520 and chrY:57443438-57772954. These sequences were taken from the corresponding regions in the X chromosome and are exact duplications of the X chromosome sequences. For further information on NCBI Build 36.1, see the NCBI Build 36.1 release notes. Bulk downloads of the data are available from the UCSC downloads server via ftp or http. We recommend that you use ftp or rsync for downloading large or multiple files. We'd like to thank NCBI and the International Human Genome Sequencing Consortium for furnishing the data, and the entire UCSC Genome Browser staff for contributing to this release. Fan Hsu led the UCSC engineering effort; QA was headed up by Ann Zweig. 6 March 2006 - Purple Sea Urchin Genome Assembly Available in Genome Browser The April 2005 release of the Purple Sea Urchin genome (Strongylocentrotus purpuratus) is now available in the UCSC Genome Browser. This assembly, UCSC version strPur1, was produced by the Baylor College of Medicine Human Genome Sequencing Center (BCM HGSC) and corresponds to their Spur_0.5 whole genome shotgun assembly. This release was assembled from whole genome shotgun reads using the Atlas genome assembly system at the BCM HGSC. Several whole genome shotgun libraries, with inserts of 2-6 kb, were used to produce the data. About 7 million reads were assembled, representing about 800 Mb of sequence and about 6x coverage of the (clonable) sea urchin genome. Highly repeated sequences were assembled separately into reptigs and merged into the genome assembly. Sequences from BAC clones were omitted from this assembly and will be placed in a subsequent version of the draft sequence. This is a draft sequence and may contain errors; therefore, users should exercise caution. Typical errors in draft genome sequences include misassemblies of repeated sequences, collapses of repeated regions, and unmerged overlaps (e.g. due to polymorphisms) creating artificial duplications. However, base accuracy in contigs (contiguous blocks of sequence) is usually very high with most errors near the ends of contigs. More assembly details can be found in the Spur_0.5 README file and on the BCM HGSC Sea Urchin Genome Project web page. Bulk downloads of the sequence and annotation data are available via the Genome Browser FTP server or the Downloads page. These data have specific conditions for use. The strPur1 annotation tracks were generated by UCSC and collaborators worldwide. See the Credits page for a detailed list of the organizations and individuals who contributed to this release. 27 February 2006 - Upcoming Genome Browser Seminars in Texas, Florida and Washington, DC The UCSC Bioinformatics Group announces four regional seminars and hands-on computer workshops on the UCSC Genome Browser, presented by OpenHelix: Houston, TX -- Tuesday, 14 March Austin, TX -- Wednesday, 15 March Washington, DC -- Tuesday, 18 April Miami, FL -- Wednesday, 19 April Two sessions will be offered each day: 9:00 a.m. to noon and 1 p.m. to 4 p.m. These introductory sessions are geared towards anyone with a basic knowledge of genomic and biological concepts who is interested in learning how to use the UCSC Genome Browser. No programming experience is required. The seminars will cover the topics necessary to learn how to effectively use the browser tool set, including basic Genome Browser functionality, searching and BLAT use, Table Browser use, creating and using custom annotation tracks, and an introduction to the Gene Sorter. Lectures will be accompanied by hands-on computer exercises conducted directly on the Genome Browser web site. Participants receive a complete set of slide and exercise handouts and printed Quick Reference Cards. For further information or to make a reservation, visit the OpenHelix website or call 1-888-861-5051. Register early; seating is limited. Academic and student discounts are available. 17 February 2006 - Zebrafish Browser Updated The latest zebrafish assembly -- Zv5 (UCSC version danRer3, May 2005) -- is now available in the UCSC Genome Browser and Blat server. The Zv5 assembly was produced by The Wellcome Trust Sanger Institute in collaboration with the Max Planck Institute for Developmental Biology in Tuebingen, Germany, and the Netherlands Institute for Developmental Biology (Hubrecht Laboratory), Utrecht, The Netherlands. This assembly consists of 1,630,306,866 bp in 16,214 scaffolds (N50 = 1,116,981 bp) with a sequence coverage of approximately 6.5-7x. The assembly has been tied to the fingerprint contig map (data freeze 15th February, 2005) and contains 699 Mb from 4,519 sequenced clones. For more information about this assembly, see the Sanger Institute web page for the Danio rerio Sequencing Project. The danRer3 sequence and annotation data can be downloaded from the UCSC Genome Browser FTP server or downloads page. Please review the guidelines for using these data. We'd like to thank the Wellcome Trust Sanger Institute, the Max Planck Institute for Developmental Biology, Hubrecht Laboratory and the other institutions who contributed to the sequencing and mapping effort of this release. Special thanks to the Zebrafish Genome Initiative at Children's Hospital in Boston for their collaboration on this release. The UCSC zebrafish Genome Browser was produced by Rachel Harte, Jennifer Jackson, Ann Zweig, Ali Sultan-Qurraie, and Donna Karolchik. The initial set of annotation tracks was generated by the UCSC Genome Bioinformatics Group. See the credits page for a detailed list of the organizations and individuals who contributed to the release of this browser. 9 February 2006 - New Rhesus Macaque Browser Released The latest rhesus macaque (Macaca mulatta) draft assembly—v.1.0, Mmul_051212—is now available in the UCSC Genome Browser. This version (UCSC rheMac2) was sequenced and assembled by the Macaque Genome Sequencing Consortium led by the Baylor College of Medicine Human Genome Sequencing Center, in collaboration with the Genome Sequencing Center at Washington University School of Medicine in St. Louis and the J. Craig Venter Institute Joint Technology Center. The rhesus macaque follows the human and chimpanzee as the third primate and first Old World monkey to have its genome sequenced. Overall, the rhesus genome shares approximately 92 to 95 precent of its sequence with the human, compared with the chimp at 98 precent. Because of its genetic, physiologic, and metabolic similarities to the human and chimp, the rhesus is an ideal reference point for comparisons among the three primates. The groups in the Macaque Genome Sequencing Consortium produced preliminary assemblies of the genome data using different and complementary approaches. The resulting data were combined into a single, high-density "melded" assembly by a team at J. Craig Venter Institute. This collaboration made use of published rhesus maps, the BAC fingerprint map from the Michael Smith Genome Sciences Centre, and the human reference genome sequence. The v.1.0 assembly covers about 93 percent of the rhesus genome. For more information about the rheMac2 assembly, see the Baylor Rhesus Monkey Project web page. The rheMac2 sequence and annotation data can be downloaded from the UCSC Genome Browser FTP server or the Downloads page. These data have specific conditions for use. Many thanks to Baylor College of Medicine, the Macaque Genome Sequencing Consortium, and the other institutions who contributed to the sequencing and mapping effort of the v.1.0 release. The UCSC Rhesus Genome Browser was produced by Robert Baertsch, Kayla Smith, Ann Zweig, Robert Kuhn, and Donna Karolchik. The initial set of rheMac2 annotation tracks was generated by the UCSC Genome Bioinformatics Group. See the credits page for a detailed list of the organizations and individuals who contributed to the release of this browser. 18 January 2006 - D. sechellia Browser Released The October 2005 D. sechellia assembly (UCSC version droSec1) is now available in the UCSC Genome Browser. This version was sequenced and assembled by the Broad Institute of MIT and Harvard. Downloads of the droSec1 data and annotations can be obtained from the UCSC Genome Browser FTP server or Downloads page. The initial set of droSec1 annotation tracks were generated by UCSC. Many thanks to the Broad Institute for providing the sequence and assembly of this genome. The UCSC D. sechellia Genome Browser was produced by Angie Hinrichs, Kayla Smith and Donna Karolchik. See the Credits page for a detailed list of the organizations and individuals who contributed to this release. 11 January 2006 - D. yakuba Browser Update The latest D. yakuba assembly is now available in the UCSC Genome Browser. This version — Release 2.0, dated Nov. 2005 (UCSC version droYak2) — was sequenced and assembled by the Genome Sequencing Center, Washington University (WUSTL) School of Medicine in St. Louis. The whole genome shotgun (WGS) assembly includes both raw shotgun data and data from two rounds of automated, directed read selection, which has improved the sequence quality and narrowed or (in some instances) closed gaps. For more assembly information and statistics, see the WUSTL Genome Sequencing Center Drosophila yakuba web page. Downloads of the droYak2 data and annotations can be obtained from the UCSC Genome Browser FTP server or Downloads page. The initial set of droYak2 annotation tracks was generated by UCSC. Thanks to the Genome Sequencing Center at WUSTL School of Medicine for providing the sequence and assembly of this genome. The droYak2 Genome Browser was produced by Angie Hinrichs, Jennifer Jackson and Donna Karolchik. See the Credits page for a detailed list of the organizations and individuals who contributed to this release. 4 January 2006 - D. persimilis Genome Browser Released The UCSC Genome Bioinformatics Group has released a Genome Browser and Blat server for the D. persimilis genome. The Oct. 2005 release (UCSC version droPer1) was sequenced and assembled by the Broad Institute of MIT and Harvard. The D. persimilis assembly joins nine other Drosophila species featured in the UCSC Genome Browser. Downloads of the droPer1 data and annotations can be obtained from the UCSC Genome Browser FTP server or Downloads page. The droPer1 annotation tracks were generated by UCSC and collaborators worldwide. Thanks to the Broad Institute for providing the sequence and assembly of this genome. The UCSC D. persimilis Genome Browser was produced by Angie Hinrichs, Kayla Smith, Robert Kuhn, Jennifer Jackson and Donna Karolchik. See the Credits page for a detailed list of the organizations and individuals who contributed to this release. 20 December 2005 - Dog Genome Browser Update Released UCSC has updated the dog Genome Browser to include the May 2005 v2.0 assembly (UCSC version canFam2) sequenced and assembled by the Broad Institute of MIT and Harvard and Agencourt Bioscience. The whole genome shotgun sequence is based on 7.6X coverage of the dog genome which includes more than 98% of the euchromatic genome. The dog genome, which contains approximately 2.5 billion base pairs, is similar in size to the genomes of humans and other mammals. The boxer breed was selected for the initial sequencing effort, based on the lower variation rate in its genome relative to other breeds. In addition to the boxer, samples from several other dog breeds were used to generate a set of single nucleotide polymorphisms (SNPs) to facilitate disease studies. The SNPs are available from the Broad Institute dog SNP web page. For more information about the dog draft assembly, see the Broad Institute Dog Genome Sequencing Project web page. The dog sequence and annotation data can be downloaded from the UCSC Genome Browser FTP server or downloads page. These data have specific conditions for use. Many thanks to the Broad Institute of MIT and Harvard, Agencourt Bioscience, and the other institutions who contributed to the sequencing, assembly, and mapping efforts. The canFam2 Genome Browser team included Angie Hinrichs, Jennifer Jackson, and Donna Karolchik. See the credits page for a detailed list of the organizations and individuals who contributed to this release. 15 December 2005 - New Mouse Assembly Available in Genome Browser The latest mouse genome assembly from the Mouse Genome Sequencing Consortium, NCBI Build 35 (UCSC version mm7), is now available in the UCSC Genome Browser. The Build 35 assembly includes approximately 2.6 Gb of sequence, of which about 2.2 Gb is finished sequence. Chromosomes 2, 4, 11 and X are finished in this build. To review in-depth statistics on the assembly, see the NCBI Build 35 Data web page. Please note that the UCSC mm7 database contains only the reference strain C57BL/6J. The mm7 sequence and annotation data may be downloaded from the Genome Browser FTP server or Downloads web page. The mm7 annotation tracks were generated by UCSC and collaborators worldwide. We'd like to thank Deanna Church and the Mouse Genome Sequencing Consortium for this assembly. We'd also like to acknowledge the work of the UCSC mm7 team: Hiram Clawson, Fan Hsu, Ann Zweig, Kayla Smith, Robert Kuhn and Donna Karolchik. For a complete list of the individuals and organizations who participated in this assembly, see the Credits page. 2 December 2005 - Announcing the VisiGene Image Browser We are pleased to announce the release of a new software tool in the Genome Browser collection, the VisiGene Image Browser. VisiGene offers the ability to view in situ images, allowing examination of expression patterns at both the tissue and cellular levels. The browser serves as a virtual microscope that lets viewers retrieve images that meet specific search criteria, then interactively zoom and scroll across the collection. The VisiGene Browser may be accessed from the menu on the UCSC Genome Bioinformatics home page or through a link on the details pages of Known Genes for which a VisiGene annotation exists. The initial release of VisiGene includes the following image collections: Mouse in situ images from the Jackson Lab Gene Expression Database (GED) Transcription factors in mouse embryos from the Mahoney Center for Neuro-Oncology Mouse head and brain in situ images from NCBI's Gene Expression Nervous System Atlas (GENSAT) database Xenopus laevis in situ images from the National Institute for Basic Biology (NIBB) XDB project We hope to integrate images from the Allen Brain Atlas into the VisiGene collection within a few months. For more information about VisiGene, visit the VisiGene Gateway page or consult the Using the VisiGene Image Browser section in the User's Guide. We'd like to thank the organizations listed above for permitting us to add their images to the VisiGene database. VisiGene was written by Jim Kent and Galt Barber of the UCSC Genome Bioinformatics Group. Contact Jim if you have an image set you'd like to contribute for display. 2 December 2005 - Allen Brain Atlas Annotation Added to Genome Browser We have released a new annotation track — Allen Brain Atlas Probes — that may be found in the Expression and Regulation section of the latest mouse and human assemblies (mm6 and hg17). The Allen Brain Atlas (ABA) is an extensive database of high resolution in situ hybridization images of adult male mouse brains covering the majority of genes. This track provides a link to the ABA images for each probe. For more information about the ABA, see the description page that accompanies this track. We'd like to thank the Allen Institute for Brain Science, and Susan Sunkin in particular, for coordinating with UCSC on this annotation. 17 October 2005 - UCSC Genome Browser Tutorial at ASHG 2005 OpenHelix will be presenting a one-hour seminar, "Introduction to the UCSC Genome Browser", at the American Society of Human Genetics (ASHG) 2005 meeting on 26 October, 6:30-7:30 p.m. The introductory tutorial will cover the topics needed to effectively use the Genome Browser, including basic search functionality and BLAT use, Table Browser use, creating and using Custom Tracks, and an introduction to the Gene Sorter. The class, which is open to all registered ASHG attendees, does not require programming skills, although a basic knowledge of genomic and biological concepts is recommended. The free tutorial will be conducted at the Grand America Hotel, Audubon Room. Snacks and beverages will be served. Attendees will receive a free download of training materials. For further information, visit www.openhelix.com or call 1-888-861-5051. 11 October 2005 - D. grimshawi Browser Now Available The UCSC Genome Bioinformatics Group has added the Drosophila grimshawi genome to the collection of fly genomes available in the UCSC Genome Browser. This assembly (UCSC version droGri1, Aug. 2005) was produced by Agencourt Bioscience Corporation in Beverly, MA, USA, using the Arachne assembler. The droGri1 assembly contains 25,052 scaffolds ranging in size from 196 bases to 14,170,260 bases. Bulk downloads of the sequence and annotation data are available via the Genome Browser FTP server or Downloads page. Please review the data use guidelines outlined in the README.txt files that accompany the downloads. The data use restrictions are also available on the Genome Browser Credits page. We'd like to thank Agencourt Bioscience Corporation for providing this assembly. The UCSC droGri1 browser was produced by Angie Hinrichs, Brian Raney, Jennifer Jackson, Kayla Smith and Donna Karolchik. The UCSC Genome Bioinformatics Group generated the initial set of annotation tracks. See the Credits page for a detailed list of the organizations and individuals who contributed to this release. 7 October 2005 - New D. ananassae Browser Released The UCSC Genome Bioinformatics Group has updated the Drosophila ananassae Genome Browser to the 1 August, 2005 assembly. This version (UCSC version droAna2) was produced by Agencourt Bioscience Corporation using the Arachne assembler. The assembly contains 13,772 scaffolds ranging in size from 55 bases to 23,697,768 bases, with a mean size of 16822.3 and median of 1537. Sequence and annotation data for the droAna2 assembly can be downloaded from the UCSC Genome Browser FTP server or downloads page. Please review the data use guidelines outlined in the README.txt files that accompany the downloads. The data use restrictions are also available on the Genome Browser credits page. We'd like to thank Agencourt Bioscience Corporation for this assembly. The UCSC droAna2 browser was produced by Angie Hinrichs, Brian Raney, Ann Zweig, Kayla Smith and Donna Karolchik. The UCSC Genome Bioinformatics Group generated the initial set of annotation tracks. See the credits page for a detailed list of the organizations and individuals who contributed to this release. 4 October 2005 - Updated Cow Browser Available The UCSC Genome Bioinformatics Group has released a Genome Browser and Blat server for the Mar. 2005 Btau_2.0 draft assembly of the cow genome. This assembly (UCSC version bosTau2) was provided by Baylor College of Medicine Human Genome Sequencing Center in Houston, TX. The Btau_2.0 release was assembled from whole genome shotgun (WGS) reads using the Atlas genome assembly system. Several WGS libraries, with inserts of 2 - 4 kb and 4 - 6 kb, were used to produce the data. Approximately 23 million reads were assembled, representing about 17.7 Gb of sequence and 6.2x coverage of the (clonable) bovine genome. Highly repeated sequences and BAC clones sequences were omitted from this assembly; these will be placed in a subsequent version of the draft sequence. The assembly contains chromosomes 1-29, X, M, and Bin0, as well as 98058 scaffolds. For details about changes UCSC made to the assembly format for display purposes, please see the bosTau2 Genome Browser gateway page. More information on the Btau_2.0 assembly can be found on the Baylor Bovine Genome Project web page. Bulk downloads of the sequence and annotation data are available via the Genome Browser FTP server or Downloads page. Please refer to the Baylor conditions of use regarding these data. The bosTau2 annotation tracks were generated by UCSC and collaborators worldwide. We'd like to thank Baylor College of Medicine for the bovine sequence and assembly. We'd also like to acknowledge the members of the UCSC Genome Bioinformatics Group who contributed to the Cow Genome Browser: Galt Barber, Brian Raney, Mark Diekhans, Jennifer Jackson and Donna Karolchik. See the Credits page for a detailed list of the organizations and individuals who contributed to this release. 20 September 2005 - Three Drosophila Assemblies Released in Genome Browser The UCSC Genome Bioinformatics Group has added three more Drosophila genomes to the collection of fly genomes in the UCSC Genome Browser. The new genomes, which include the initial assembly of D. erecta (droEre1, Aug. 2005) and the updated assemblies of D. virilis (droVir2, Aug. 2005) and D. mojavensis (droMoj2, Aug. 2005), were produced by Agencourt Bioscience Corporation in Beverly, MA, USA. All three genomes were assembled using the Arachne assembler. The droEre1 assembly contains 5,124 scaffolds ranging in size from 154 bases to 26,647,023 bases, with a mean size of 29832.7 and median of 1740. The droVir2 assembly consists of 13,562 scaffolds ranging in size from 57 bases to 25,269,527 bases, with a mean size of 15263.1 and median of 1249. The droMoj2 assembly is comprised of 6,843 scaffolds ranging in size from 101 bases to 34,172,700 bases, with a mean size of 28389.6 and median of 1671. Bulk downloads of the sequence and annotation data are available from the UCSC downloads server: droEre1 - FTP, HTTP droVir2 - FTP, HTTP droMoj2 - FTP, HTTP Please review the data use guidelines outlined in the README.txt files that accompany the downloads. The data use restrictions are also available on the Genome Browser credits page. We'd like to thank Agencourt Bioscience Corporation for providing these assemblies. The UCSC Drosophila browsers were produced by Angie Hinrichs, Brian Raney, Jennifer Jackson and Donna Karolchik. The UCSC Genome Bioinformatics Group generated the initial set of annotation tracks. See the credits page for a detailed list of the organizations and individuals who contributed to this release. 9 September 2005 - C. intestinalis v2.0 Genome Browser Released The v2.0 C. intestinalis draft assembly from the US DOE Joint Genome Institute (JGI) is now available in the UCSC Genome Browser and Blat server (UCSC database ci2). This whole genome shotgun assembly was constructed with the JGI assembler, JAZZ, using paired-end sequencing reads. Starting with a coverage of 11x, additional data -- including BAC and FISH markers -- were used to map scaffolds to chromosome arms. The size of this assembly, including unmapped scaffolds, is 173 Mb, with 94 Mb of the sequence mapped to chromosome arms. For more information about the ci2 assembly, see the JGI C. intestinalis project page. Additional information and an analysis of the euchromatic regions of this genome may be found in Dehal, P. et al. The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins. Science 298(5601), 2157-67 (2002). Bulk downloads of the sequence and annotation data are available via the Genome Browser FTP server or Downloads page. The ci2 annotation tracks were generated by UCSC and collaborators worldwide. See the Credits page for a detailed list of the organizations and individuals who contributed to this release. Many thanks to the JGI and their collaborators for providing the v2.0 sequence and annotations. The ci2 Genome Browser was produced by Brian Raney, Mark Diekhans, Ann Zweig, Kayla Smith, Robert Kuhn and Donna Karolchik. 11 August 2005 - Upcoming Genome Browser Seminars - San Francisco, Seattle, Chicago, Boston, Philadelphia, Atlanta The UCSC Bioinformatics Group announces six regional seminars and hands-on computer workshops on the UCSC Genome Browser, presented by OpenHelix: San Francisco -- Monday, 22 August Seattle -- Wednesday, 24 August Chicago -- Tuesday, 27 September Boston -- Wednesday, 28 September Philadelphia -- Tuesday, 15 November Atlanta -- Wednesday, 16 November These introductory sessions are geared towards anyone with a basic knowledge of genomic and biological concepts who is interested in learning how to use the UCSC Genome Browser. No programming experience is required. The seminars will cover the topics necessary to learn how to effectively use the browser tool set, including basic Genome Browser functionality, searching and BLAT use, Table Browser use, creating and using custom annotation tracks, and an introduction to the Gene Sorter. Lectures will be accompanied by hands-on computer exercises conducted directly on the Genome Browser web site. For location and registration information, visit the OpenHelix website or call 1-888-861-5051. Academic and student discounts are available. Posted on 13 June 2005 - Drosophila simulans Genome Browser Released The UCSC Genome Bioinformatics Group has released a Genome Browser for the Drosophila simulans draft genome sequence. The Release 1.0 assembly (UCSC version droSim1, April 2005) was produced by the Genome Sequencing Center at the Washington University in St. Louis (WUSTL) School of Medicine. Release 1.0 represents a composite of several different D. simulans lines: contigs from the w501 line comprise the primary scaffolding, with contigs and unplaced reads from six other lines used to fill gaps in the w501 assembly. The total size of this assembly, excluding the gapless 14,972 bp mitochondrial sequence, is 142,405,747 bp including gaps and 127,241,461 bp excluding gaps. For more information about the D. simulans assembly and statistics, see the WUSTL Genome Sequencing Center Drosophila simulans web page. Downloads of the droSim1 data and annotations may be obtained from the UCSC Genome Browser FTP server or Downloads page. The droSim1 annotation tracks were generated by UCSC and collaborators worldwide. Thanks to the Genome Sequencing Center, WUSTL School of Medicine for providing this assembly. We'd also like to acknowledge the UCSC team who worked on this release: Angie Hinrichs, Jennifer Jackson, Ali Sultan-Qurraie, Brian Raney and Donna Karolchik. See the Credits page for a detailed list of the organizations and individuals who contributed to this release. Posted on 31 May 2005 - June Genome Browser Seminars in San Diego, CA and Salt Lake City, UT The UCSC Bioinformatics Group announces two seminars and hands-on workshops on the UCSC Genome Browser, presented by OpenHelix, a bioinformatics training, software testing and consulting company. These introductory sessions are geared towards anyone with a basic knowledge of genomic and biological concepts who is interested in learning how to use the UCSC Genome Browser. No programming experience is required. The seminars will cover the topics necessary to learn how to effectively use the browser tool set, including basic Genome Browser functionality, searching and BLAT use, Table Browser use, creating and using custom annotation tracks, and an introduction to the Gene Sorter. Lectures will be accompanied by hands-on computer exercises conducted directly on the Genome Browser web site. The first three-hour course will be held on Thursday 9 June in the Salt Lake City, UT area. Two sessions will be offered: 9am-12pm and 1pm-4pm. The second seminar will be held in San Diego, CA on Friday, 10 June. Two sessions will be offered: 9am-12pm and 1pm-4pm. For registration information, visit the OpenHelix website or call 1-888-861-5051. Academic and student discounts are available. Posted on 18 May 2005 - Rhesus Monkey Genome Browser Released The UCSC Genome Bioinformatics group has released a Genome Browser for the rhesus monkey draft assembly, Mmul_0.1 (UCSC version rheMac1), produced by the Baylor College of Medicine Human Genome Sequencing Center in collaboration with J. Craig Venter Science Foundation Joint Technology Center and the Genome Sequencing Center at Washington University School of Medicine in St. Louis. This Old World monkey, which is a primate model organism, is important for the study of human biology and disease due to its genetic, physiologic and metabolic similarities to humans. Mmul_0.1 is a preliminary assembly using whole genome shotgun (WGS) reads from small and medium insert clones. Approximately 14.6 million reads were used in the assembly, representing about 12.6 Gb of sequence and about 4.6x coverage of the (clonable) genome. The total length of all contigs is approximately 2.7 Gb, or 2.8 Gb including gaps between contigs. Highly-repeated sequences and sequences from BAC clones were omitted from this assembly and will be placed in a subsequent version of the draft sequence. For more information about the rheMac1 assembly, see the Baylor Rhesus Monkey Project web page. The rheMac1 sequence and annotation data can be downloaded from the UCSC Genome Browser FTP server or the Downloads page. These data have specific conditions for use. Many thanks to Baylor College of Medicine, the Rhesus Monkey Genome Sequencing Consortium, and the other institutions who contributed to the sequencing and mapping effort of the Mmul_0.1 release. The UCSC Rhesus Genome Browser was produced by Robert Baertsch, Galt Barber, and Donna Karolchik. The initial set of rheMac1 annotation tracks was generated by the UCSC Genome Bioinformatics Group. See the credits page for a detailed list of the organizations and individuals who contributed to the release of this browser. Posted on 5 May 2005 - New Mouse Assembly Available in Genome Browser The latest mouse genome assembly from the Mouse Genome Sequencing Consortium, NCBI Build 34 (UCSC version mm6), is now available in the UCSC Genome Browser. In conjunction with this release, we have archived mouse assemblies mm3 and mm4. All archived assemblies are accessible on our archive server. The Build 34 assembly has an assembled length of approximately 2.6 Gb, of which about 1.9 Gb is finished sequence. Chromosomes 2, 4, 11 and X are finished in this build. To review in-depth statistics on the assembly, see the NCBI Build 34 Data web page. NOTE: In the Genome Browser mm6 assembly, chrY_random erroneously contains a region duplicated from chrY. For more information about this issue, see the Genome Browser FAQ. Please also note that the UCSC mm6 database contains only the reference strain C57BL/6J. The mm6 sequence and annotation data may be downloaded from the Genome Browser FTP server or Downloads web page. The mm6 annotation tracks were generated by UCSC and collaborators worldwide. Mirror sites, please note: due to the size of the comparative genomics annotations in this assembly, the data set requires an unusually large amount of disk space. If you regularly download updates of the mouse data to your site, you may want to examine your available disk space before adding the annotation database from this assembly and/or reschedule your download for a period of low activity on your server. The size of the mm6 annotation database directory ($WEBROOT/goldenPath/mm6/database/) is approximately 93 GB. Including the related net and chains, the total size is 124 GB. We'd like to thank Deanna Church and the Mouse Genome Sequencing Consortium for this assembly. We'd also like to acknowledge the work of the UCSC mm6 team: Hiram Clawson, Fan Hsu, Jennifer Jackson, Robert Kuhn, Ali Sultan-Qurraie, Heather Trumbower and Donna Karolchik. For a complete list of the individuals and organizations who participated in this assembly, see the Credits page. Posted on 2 May 2005 - Archiving mm3 and mm4 assemblies To make room for the NCBI Build 34 mouse assembly (mm6, March 2005), we are archiving the mm3 and mm4 mouse assemblies. These assemblies will remain available on our archive server, although blat will no longer be supported. We plan to release the mm6 assembly in the next day or so. Posted on 24 Mar. 2005 - Genome Browser Tutorial at Experimental Biology 2005 on 5 April OpenHelix will be presenting a one-hour introductory seminar on the UCSC Genome Browser at the Experimental Biology 2005 meeting on 5 April, 5:00-6:00. The tutorial will cover the topics needed to effectively use the Browser, including basic functionality, searching and BLAT use, Table Browser use, creating and using Custom Tracks, and an introduction to the Gene Sorter. The free session will be conducted at the San Diego Convention Center, Room 12. For further information, visit the OpenHelix website or call 1-888-861-5051. OpenHelix will also be presenting brief introductory overviews of the UCSC Genome Browser in its Experimental Biology booth #133-135 during show hours. Stop by the booth for more information and to receive your free UCSC Quick Reference Card. Posted on 2 Mar. 2005 - CCDS Data Set Released The initial results from the Consensus Coding Sequence project (CCDS) were released to the public today. CCDS is a collaborative effort to identify a core set of human protein-coding regions that are consistently annotated and of high quality. The initial CCDS data set, containing nearly 15,000 transcripts, has been posted on three Internet sites: the UCSC Genome Browser, the Ensembl Browser and the NCBI CCDS Database website. The genes may be viewed on the UCSC hg17 (May 2004) Human Genome Browser in the CCDS annotation track located in the Genes and Gene Prediction Tracks section. The CCDS gene set is built by consensus among the following collaborating organizations: European Bioinformatics Institute (EBI) National Center for Biotechnology Information (NCBI) University of California Santa Cruz (UCSC) Wellcome Trust Sanger Institute (WTSI) Each gene in the CCDS set is assigned a unique identifier and version number, e.g. CCDS234.1. The version number will be updated if either the CDS structure or the underlying genome sequence at that location changes. The CCDS set will be mapped forward, with identifiers preserved, when the annotations or sequence update. Changes to existing CCDS genes will be done by collaboration agreement; no single group will change the set unilaterally. CCDS identifiers are included on relevant NCBI RefSeq and Entrez Gene records. Gene structure information is obtained from both curated and automated genes sources. The primary curation groups are the Havana team at the WTSI and the RefSeq annotation group at NCBI. In addition, manually curated information on chr14 (Genoscope) and Chr7 (WUSTL) has been included from the Vega database. The Ensembl group and the RefSeq computational pipeline provide the automated data. Curated information is favored over automated information; the information must be consistent between the Hinxton (Vega/Ensembl) and NCBI groups and also pass UCSC's stringent QC requirements. At a minimum, a gene must meet three quality criteria to be included in the CCDS set: The coding region has a full-length annotation with an initiating ATG, a valid stop codon, and no in-frame stop codons. Protein can be translated from the genome without frameshifts. Consensus splice-sites are used. For more information on the process used to identify and evaluate CCDS genes, refer to the description page for the Genome Browser CCDS track. The number and type of quality tests performed may be expanded in the future, but includes analysis to identify putative pseudogenes, retrotransposed genes, consensus splice sites, supporting transcripts, and protein homology. The completeness of the CCDS gene set should improve as the curation and automated annotation processes mature and additional experimental validation is obtain for weakly-supported genes. UCSC would like to thank EBI, NCBI and WTSI for their collaboration in the release of these data. We would also like to acknowledge the efforts of the UCSC staff who worked on this project: Mark Diekhans, Robert Baertsch, Adam Siepel, Fan Hsu, and Robert Kuhn. Posted on 24 Feb. 2005 - Genome Browser Training - St. Louis and NYC We'd like to announce upcoming UCSC Genome Browser seminars and hands-on computer workshops in St. Louis, MO, and New York, NY, presented by OpenHelix, the bioinformatics training, software testing and consulting company. These introductory tutorials will cover the topics needed to effectively use the browser, including basic functionality of Genome Browser searching and BLAT use, Table Browser use, creating and using Custom Tracks, and an introduction to the Gene Sorter. The St. Louis class will be held on 29 March, 2005 at the Object Computing, Inc. training center. Two sessions will be offered: 9 a.m. - 12 p.m. and 1 - 4 p.m. The New York City class will be held on 30 March, 2005 at the ThinkPath Training facility. Two sessions will be offered: 9 a.m. - 12 p.m. and 1 - 4 p.m. For more information about class locations, costs, and registration, visit the OpenHelix website or call 1-888-861-5051. Academic, student, and early registration discounts are available. Posted on 23 Feb. 2005 - New Honeybee Genome Browser The UCSC Genome Bioinformatics group has released a Genome Browser for a second honeybee assembly, Amel_2.0 (UCSC version apiMel2), produced by the Baylor College of Medicine Human Genome Sequencing Center. The assembly -- which is approximately 229 Mb in size including contig gaps -- was sequenced using a combined whole genome shotgun (WGS) and BAC clone approach. Overall sequence coverage is estimated at 7.5x. In this assembly, scaffolds have been arranged into 17 linkage groups that are somewhat equivalent to chromosomes. For more information about the assembly, see the Baylor honeybee project website. The apiMel2 sequence and annotation data can be downloaded from the UCSC Genome Browser FTP server or downloads page. Please see the Baylor conditions of use page for guidelines regarding the use of these data. Many thanks to Baylor College of Medicine and the other institutions who contributed to the sequencing and mapping effort of the Amel_v2.0 release. The UCSC A. mellifera Genome Browser was produced by Andy Pohl, Angie Hinrichs, Jennifer Jackson, and Donna Karolchik. The initial set of apiMel2 annotation tracks was generated by the UCSC Genome Bioinformatics Group. See the credits page for a detailed list of the organizations and individuals who contributed to the release of this browser. Posted on 17 Feb. 2005 - Cow Genome Browser Released The UCSC Genome Bioinformatics Group has released a Genome Browser and Blat server for the Sep. 2004 Btau_1.0 draft assembly of the cow genome. This assembly (UCSC version bosTau1) was provided by Baylor College of Medicine Human Genome Sequencing Center in Houston, TX. The Btau_1.0 release was assembled from whole genome shotgun (WGS) reads using the Atlas genome assembly system. Several WGS libraries, with inserts of 2 - 4 kb and 4 - 6 kb, were used to produce the data. Approximately 15 million reads were assembled, representing about 9 Gb of sequence and 3x coverage of the (clonable) bovine genome. Highly repeated sequences and BAC clones sequences were omitted from this assembly; these will be placed in a subsequent version of the draft sequence. The assembly contains approximately 450,000 scaffolds. For more information on the Btau_1.0 assembly, see the Baylor Bovine Genome Project web page. Bulk downloads of the sequence and annotation data are available via the Genome Browser FTP server or Downloads page. Please refer to the Baylor conditions of use regarding these data. The bosTau1 annotation tracks were generated by UCSC and collaborators worldwide. We'd like to thank Baylor College of Medicine for the bovine sequence and assembly. We'd also like to acknowledge the members of the UCSC Genome Bioinformatics Group who contributed to the Cow Genome Browser: Heather Trumbower, Jim Kent, Hiram Clawson, Angie Hinrichs, Brian Raney, Mark Diekhans, Robert Kuhn, Ali Sultan-Qurraie, and Donna Karolchik. See the Credits page for a detailed list of the organizations and individuals who contributed to this release. Posted on 15 Feb. 2005 - UniProt (Swiss-Prot/TrEMBL) Display Changes We have made several adjustments to the Genome Browser databases to accommodate recent changes to display IDs introduced by UniProt (aka Swiss-Prot/TrEMBL). If you are using the proteinID field in our knownGene table or the Swiss-Prot/TrEMBL display ID for indexing or cross-referencing other data, we strongly suggest you transition to the UniProt accession number. These changes will also affect anyone who is mirroring our site. To review a detailed list of the changes to the Genome Browser databases, see our FAQ. Posted on 14 Feb. 2005 -D. melanogaster Release 4 Now Available The D. melanogaster Release 4 assembly (UCSC version dm2, Apr. 2004) is now available in the Genome Browser. This version includes Release 4 euchromatic sequence from the Berkeley Drosophila Genome Project (BDGP), Release 3.2 heterochromatic genome sequence from the Drosophila Heterochromatin Genome Project (DHGP), and Release 4.0 annotations (dated Nov. 2004) from FlyBase. Insects in the UCSC Genome Browser collection include six Drosophila genomes, the honeybee, and Anopheles gambiae. The Release 4 euchromatic sequence, 118.4 Mb in size, contains six euchromatic chromosome arms with a total of 23 sequence gaps. The assembly was validated in collaboration with the Genome Sciences Centre at the British Columbia Cancer Agency in Vancouver, Canada, using fingerprint analysis of a tiling path of BACs spanning the genome. The Release 3.2 heterochromatic sequence is based on 20.7 Mb of Release 3 whole genome shotgun scaffolds from Celera that could not be assembled into the euchromatin arms, as well as a few BDGP-sequenced scaffolds. The scaffolds have been assigned to chromosomes where possible. For more information on this assembly, see the release notes for the Release 4 euchromatic sequence and Release 3.2 heterochromatic sequence. Downloads of the dm2 data and annotations may be obtained from the UCSC Genome Browser FTP server or Downloads page. The dm2 annotation tracks were provided by FlyBase or generated by UCSC. Thanks to BDGP, DHGP, and the Flybase Consortium for providing the sequence, assembly, gene annotations and analysis of this genome. The UCSC Genome Browser team is Angie Hinrichs, Brian Raney, Galt Barber, and Donna Karolchik. See the Credits page for a detailed list of the organizations and individuals who contributed to this release. Posted on 18 Jan. 2005 - Opossum Genome Browser The opossum (Monodelphis domestica) is the latest vertebrate addition to the UCSC Genome Browser genome collection. The Oct. 2004 preliminary assembly -- UCSC version monDom1 -- was sequenced and assembled by The Broad Institute, Cambridge, MA, USA. This preliminary draft was assembled from 33,507,069 placed reads, and consists of 109,065 contigs containing a total of 3,492,108,230 bases. There are 3,563,247,205 total bases in the 19,348 scaffolds in the assembly, with 71,138,975 bases in the gaps between contigs within the scaffolds. The scaffolds range in size from 1,000 bases to 22,286,839 bases. The monDom1 sequence and annotation data can be downloaded from the UCSC Genome Browser FTP server or downloads page. Please review the guidelines for using these data. Many thanks to The Broad Institute for providing these data. The UCSC opossum Genome Browser was produced by Hiram Clawson, Galt Barber, Ali Sultan-Qurraie, Brian Raney and Donna Karolchik. The initial set of annotation tracks was generated by the UCSC Genome Bioinformatics Group. See the credits page for a detailed list of the organizations and individuals who contributed to the release of this browser. Posted on 23 Dec. 2004 - Updated Zebrafish Assembly (Zv4) Now Available The latest zebrafish assembly -- Zv4 (UCSC version danRer2, June 2004) -- is now available in the UCSC Genome Browser and Blat server. The Zv4 assembly was produced by The Wellcome Trust Sanger Institute in collaboration with the Max Planck Institute for Developmental Biology in Tuebingen, Germany, and the Netherlands Institute for Developmental Biology (Hubrecht Laboratory), Utrecht, The Netherlands. This assembly consists of 1,560,480,686 bp in 21,333 scaffolds with a sequence coverage of approximately 5.7x. 443 Mb of the assembly is from 2,828 finished clones and 121 Mb is from 1,272 unfinished clones. 75% of the sequence was tied to the fingerprint contig (FPC) map, which provided a template for placing the unfinished sequence. The remaining sequence was filled with whole genome shotgun (WGS) contigs using a combination of sequence alignment and BAC end positions. The WGS contigs used in this assembly were identical to those used for the Zv3 assembly, but the FPC data and its integration with the WGS data has been considerably improved. The Sanger Institute notes that there is high level of misassembly present in this release due to the large amount of polymorphism in the DNA source. Highly variable regions within the genome posed assembly difficulties, most likely because the sequences originated from different haplotypes. For more information about this assembly, see the Sanger Institute web page for the Danio rerio Sequencing Project. In addition to the assembly improvements noted above, a new zebrafish repeat library was used to mask repeats in the danRer2 Genome Browser, resulting in a cleaner set of alignments containing considerably less "noise". The danRer2 sequence and annotation data can be downloaded from the UCSC Genome Browser FTP server or downloads page. Please review the guidelines for using these data. We'd like to thank the Wellcome Trust Sanger Institute, the Max Planck Institute for Developmental Biology, Hubrecht Laboratory and the other institutions who contributed to the sequencing and mapping effort of this release. Special thanks to the Zebrafish Genome Initiative at Children's Hospital in Boston for their collaboration on this release. The UCSC zebrafish Genome Browser was produced by Rachel Harte, Mark Diekhans, Heather Trumbower, Jennifer Jackson, and Donna Karolchik. The initial set of annotation tracks was generated by the UCSC Genome Bioinformatics Group. See the credits page for a detailed list of the organizations and individuals who contributed to the release of this browser. Posted on 22 Dec. 2004 - UCSC Releases Honeybee Browser The UCSC Genome Bioinformatics group has released a Genome Browser for the Amel_1.2 honeybee assembly produced by the Baylor College of Medicine Human Genome Sequencing Center. The assembly -- which is approximately 213 Mb in size including contig gaps -- was sequenced using a combined whole genome shotgun (WGS) and BAC clone approach. The BAC clone sequence was produced following a pooled-array strategy. Overall sequence coverage is estimated at 6X. For more information about this assembly, see the Baylor honeybee project website. The honeybee genome is of interest to the agricultural community, in addition to its role as a model organism in the study of several human health issues, including immunity, allergic reaction, antibiotic resistance, development, mental health, longevity, and diseases of the X chromosome. The honeybee is also interesting for its social and behavioral traits. The apiMel1 sequence and annotation data can be downloaded from the UCSC Genome Browser FTP server or downloads page. Please see the Baylor conditions of use page for guidelines regarding the use of these data. Many thanks to Baylor, Children's Hospital Oakland Research Institute (CHORI), and the other institutions who contributed to the sequencing and mapping effort of the Amel_1.2 release. The UCSC A. mellifera Genome Browser was produced by Angie Hinrichs, Brian Raney, Robert Kuhn, and Donna Karolchik. The initial set of apiMel1 annotation tracks was generated by the UCSC Genome Bioinformatics Group. See the credits page for a detailed list of the organizations and individuals who contributed to the release of this browser. Posted on 15 Dec. 2004 - Three New Drosophila Assemblies in Genome Browser The UCSC Genome Bioinformatics Group has added three more Drosophila genomes to the UCSC Genome Browser. The new genomes -- initial assemblies of D. ananassae (droAna1, Jul. 2004), D. virilis (droVir1, Jul. 2004), and D. mojavensis (droMoj, Aug. 2004) -- join the D. melanogaster, D. yakuba, and D. pseudoobscura genomes already in the collection. The D. virilis and D. mojavensis genomes were sequenced and assembled by Agencourt Bioscience Corporation using the Arachne assembler. The Institute of Genomic Research (TIGR) produced the D. ananassae assembly using the Celera assembler. For more details about an individual genome, refer to the Genome Browser gateway page associated with the assembly. In upcoming months, UCSC plans to provide several additions and enhancements to the Drosophila browsers: - additional Drosophila genomes, including D. erecta and D. simulans - updated versions of D. melanogaster and other genomes - multiple alignments of all fly assemblies from the 12-Drosophila project to D. melanogaster Sequence and annotation data for all the Drosophila assemblies can be downloaded from the UCSC Genome Browser FTP server or downloads page. Please review the data use guidelines outlined in the README.txt files that accompany the downloads. The data use restrictions are also available on the Genome Browser credits page. We'd like to thank Agencourt Bioscience Corporation, TIGR, and other institutions who contributed to the sequencing and mapping effort for these assemblies. The UCSC Drosophila browsers were produced by Angie Hinrichs, Brian Raney, Heather Trumbower, Robert Kuhn, Galt Barber, Jennifer Jackson, Ali Sultan-Qurraie, and Donna Karolchik. The UCSC Genome Bioinformatics Group generated the initial set of annotation tracks. See the credits page for a detailed list of the organizations and individuals who contributed to this release. Posted on 3 Dec. 2004 - SNP Track for Build 35 (hg17) Assembly Released UCSC has released the much-awaited SNP annotation track for the Build 35 (hg17) Human Genome Browser. The SNP data were obtained from dbSnp Build 123, the first dbSnp release based on the latest human assembly. In conjunction with the data release, we have made several improvements to the graphical display of the track. Our users now have the ability to filter the SNP data based on validation status, functional class, variant class, average heterozygosity and other features. Variants may be drawn in user-selected colors to highlight additional details in the graphical image. Also, the browser now displays all SNP variants at the appropriate base width, rather than as generic ticks. Posted on 17 Nov. 2004 - X. tropicalis v.3.0 Released in Genome Browser The v.3.0 Xenopus tropicalis assembly is now available on the UCSC Genome Browser. This whole genome shotgun assembly (xenTro1, October 2004) was provided by the U.S. DOE Joint Genome Institute (JGI). Version 3.0 was constructed with the JGI assembler, Jazz, using paired end sequencing reads at a coverage of 7.4X. After trimming for vector and quality, 19.1 million reads assembled into 27,064 scaffolds totaling 1.63 Gbp. Roughly half the genome is contained in 392 scaffolds, each of which is at least 1.2 Mb in length. For more information about this assembly, see the JGI X. tropicalis website. The xenTro1 sequence and annotation data can be downloaded from the UCSC Genome Browser FTP server or downloads page. Please see the JGI data release policy for data use guidelines. Many thanks to JGI and the other institutions who contributed to the sequencing and mapping effort of the v. 3.0 release. The UCSC X. tropicalis Genome Browser was produced by Fan Hsu, Jim Kent, Heather Trumbower, Hiram Clawson, Brian Raney, Galt Barber, Mark Diekhans, Angie Hinrichs, and Donna Karolchik. The initial set of xenTro1 annotation tracks was generated by the UCSC Genome Bioinformatics Group. See the credits page for a detailed list of the organizations and individuals who contributed to the release of this browser. Posted on 17 Nov. 2004 - Genome Browser Tutorial Offered at ASCB Meeting OpenHelix will be presenting the tutorial "Introduction to the UCSC Genome Browser" at the American Society for Cell Biology (ASCB) Annual Meeting in Washington, D.C. on 5 Dec., 8:30 - 10:00 p.m. This introductory session will cover the topics needed to effectively use the Genome Browser, including basic functionality of Genome Browser searching and BLAT use, Table Browser use, creating and using Custom Tracks, and an introduction to the Gene Sorter. The free 1-1/2-hour tutorial will be conducted at the Washington Convention Center, Room 206. OpenHelix will also be presenting brief introductory overviews of the UCSC Genome Browser in its ASCB booth #510-512 during show hours. Stop by the booth for more information and to receive your free UCSC Quick Reference Card. For more information about the tutorial and other services offered by OpenHelix, visit www.openhelix.com or call 1-888-861-5051. Posted on 8 Oct. 2004 - Updated Proteome Browser Released UCSC has released v1.1 of the UCSC Proteome Browser. This updated version includes the following major enhancements: direct access to a Proteome Browser gateway via the "Proteome Browser" menu link on the Genome Browser home page. The Proteome Browser gateway page prompts the user for a protein ID or gene symbol, then directly starts up the Proteome Browser, eliminating the multiple Genome Browser steps required by the previous release. extended protein coverage that includes all proteins in the Swiss-Prot/TrEMBL databases, rather than just the human, mouse and rat protein sets included in the previous version. In addition to providing direct access to the Proteome Browser, the v1.1 release preserves the existing tight coupling between the Proteome Browser and the Genome Browser for the human, mouse and rat genomes. Users may still navigate between the Genome Browser Known Genes track and the Proteome Browser for quick, easy access to the details of a gene's genomic and proteomic sequence structures. The UCSC team who worked on the Proteome Browser update includes Fan Hsu, Robert Kuhn, Donna Karolchik and Tom Pringle. Please send comments or questions to our mailing list at genome@soe.ucsc.edu. Posted on 5 Oct. 2004 - East Coast Genome Browser Seminars - Nov. 2004 The UCSC Bioinformatics Group announces two seminars and hands-on workshops on the UCSC Genome Browser, presented by OpenHelix, a bioinformatics training, software testing and consulting company. These introductory sessions are geared towards anyone with a basic knowledge of genomic and biological concepts who is interested in learning how to use the UCSC Genome Browser. No programming experience is required. The seminars will cover the topics necessary to learn how to effectively use the browser tool set, including basic Genome Browser functionality, searching and BLAT use, Table Browser use, creating and using custom annotation tracks, and an introduction to the Gene Sorter. Lectures will be accompanied by hands-on computer exercises conducted directly on the Genome Browser web site. The first three-hour course will be held on Tuesday 9 November in the Washington, D.C. area. Two sessions will be offered: 9am-12pm and 1pm-4pm. The second seminar will be held in the Raleigh/Durham, N.C. area on Wednesday, 10 November. Two sessions will be offered: 9am-12pm and 1pm-4pm. For registration information, visit the OpenHelix website or call 1-888-861-5051. Academic, student, and early registration discounts are available. Posted on 1 Oct. 2004 - UCSC Releases New Table Browser We are pleased to announce the release of an enhanced version of the UCSC Table Browser. This new release sports several improvements and additions over the previous Table Browser, including: a new streamlined user interface support for generating filters that include fields from multiple tables, including those from non-positional tables an enhanced schema-viewing utility that displays all tables associated with a track, as well as all tables linked to a selected table the ability to restrict queries to include only data from ENCODE regions the addition of a GALA output option an option to save large output results sets directly to a file rather than displaying them in the Table Browser The preliminary User's Guide will be enhanced in upcoming weeks to include examples of many common Table Browser queries generated by our users. The new version of the Table Browser was produced by Jim Kent, Donna Karolchik, Heather Trumbower, Hiram Clawson, and Robert Kuhn, and incorporates code from the previous version written by Angie Hinrichs. We'd like to thank Mary Mangan and others on the OpenHelix staff for their feedback on early versions of this software. The older version of the Table Browser will remain available for a limited time at http://genome.ucsc.edu/cgi-bin/hgText. Please send feedback and questions to our mailing list at genome@soe.ucsc.edu. Posted on 10 Sep. 2004 - T. nigroviridis Genome Now Available in Genome Browser The Genoscope v7 Tetraodon nigroviridis genome assembly is now available in the UCSC Genome Browser and Blat server. This assembly, UCSC version tetNig1 dated Feb. 2004, is the result of a collaboration between Genoscope and the Broad Institute of MIT and Harvard. The v7 assembly was constructed using the whole genome shotgun (WGS) approach, resulting in a sequence coverage of about 7.9X. The assembly contains 45,609 contigs and 25,773 scaffolds generated by the Arachne program and covers more than 90% of the genome. Additional linking data were used to build ultracontigs and to organize the assembly into chromosomes. Genoscope estimates the size of the Tetraodon genome to be about 385 Mb. Downloads of the tetNig1 data and annotations may be obtained from the UCSC Genome Browser FTP server or Downloads page. These data have been freely provided by Genoscope before publication with specific conditions for use. The initial set of annotation tracks were generated by Genoscope and the UCSC Bioinformatics Group based on data provided Genoscope. Tetraodon gene predictions generated by Genoscope using GAZE will be available in the Genome Browser within a few weeks. Many thanks to Genoscope and the Broad Institute of MIT and Harvard for this genome assembly. The UCSC team who produced this browser are Rachel Harte, Robert Kuhn, Donna Karolchik, and the Genome Browser sysadmin team. See the Credits page for a detailed list of the organizations and individuals who contributed to this release. Posted on 1 Sep. 2004 - Genome Browser Released for D. pseudoobscura Draft Assembly The UCSC Genome Bioinformatics Group has released a Genome Browser and Blat server for the Drosophila pseudoobscura Freeze 1 draft assembly (Aug. 2003). This assembly, UCSC version dp2, was produced by the Human Genome Sequencing Center (HGSC) at Baylor College of Medicine. Freeze 1 is a whole genome shotgun assembly produced using Baylor HGSC's assembly engine, Atlas. The assembly, which provides approximately 7x coverage of the euchromatic portion of the genome, contains 759 scaffolds. The scaffold N50 size is 1,018,646 bp. The total scaffold size for this assembly is 139.3 Mbp, with an average size of 184,465 bp. Due to an assembly error, four large scaffolds "jumped" chromosomes. These have been split into "A" and "B" parts in the downloadable assembly files. See the gateway page for more information. Baylor HGSC has provided a putative chromosome assignment for the majority of larger scaffolds (> 90% of unique sequence), based on conservation between the Muller elements. Downloads of the dp2 data and annotations may be obtained from the UCSC Genome Browser FTP server or Downloads page. The initial set of annotation tracks were generated by UCSC. Many thanks to the Baylor HGSC for providing the genome assembly data. The UCSC team who produced this browser are Angie Hinrichs, Heather Trumbower, Robert Kuhn, Donna Karolchik, and the Genome Browser sysadmin team. See the Credits page for a detailed list of the organizations and individuals who contributed to this release. Posted on 30 Aug. 2004 - Genome Browser Seminars - Seattle and San Francisco The UCSC Bioinformatics Group announces 2 seminars and hands-on workshops on the UCSC Genome Browser, presented by OpenHelix, a bioinformatics training, software testing and consulting company. These introductory sessions are geared towards anyone with a basic knowledge of genomic and biological concepts who is interested in learning how to use the UCSC Genome Browser. No programming experience is required. The seminars will cover the topics necessary to learn how to effectively use the browser tool set, including basic Genome Browser functionality, searching and BLAT use, Table Browser use, creating and using custom annotation tracks, and an introduction to the Gene Sorter. Lectures will be accompanied by hands-on computer exercises conducted directly on the Genome Browser web site. The first three-hour course will be held on Monday 4 October in Kirkland, WA (Seattle area). Two sessions will be offered: 9:00 a.m. - noon or 1 - 4 p.m. The second seminar will be held in Cupertino (San Francisco Bay Area) on Tuesday, 5 October. Two sessions will be offered: 1 - 4 p.m. or 6 - 9 p.m. For registration information, visit the OpenHelix website or call 1-888-861-5051. Academic, student, and early registration discounts are available. Posted on 10 Aug. 2004 - Genome Browser Released for A. gambiae Draft Genome The UCSC Genome Bioinformatics Group has released a Genome Browser and Blat server for the Anopheles gambiae v. MOZ2 draft genome sequence (Feb. 2003). This assembly -- UCSC version anoGam1 -- was produced by the International Anopheles Genome Project and downloaded from Ensembl. The MOZ2 assembly is a 10x whole genome shotgun assembly. The assembled portion of the genome is about 278 Mbp in length with a total of 8,987 unique scaffolds, the largest scaffold being 23.1 Mbp. Approximately 85% of the sequence has been assigned to chromosomal locations. Chromosome arms chr2L, chr2R, chr3L, chr3R, and chrX are represented by 13, 49, 42, 28, and 10 large scaffolds respectively. No scaffolds have yet been assigned to the Y chromosome. The unassigned scaffolds, concatenated together in arbitrary order, can be found in the artificial unknown "chromosome" chrUn. For more information about the initial A. gambaie assembly, see Holt et al. (2002), The Genome Sequence of the Malaria Mosquito Anopheles gambiae, Science 2002 298:129-149. Downloads of the anoGam1 data and annotations may be obtained from the UCSC Genome Browser FTP server or Downloads page. The anoGam1 annotation tracks were generated by UCSC and collaborators worldwide. Many thanks to the International Anopheles Genome Project and Ensembl for providing the sequence of this genome. The UCSC team who produced this browser are Angie Hinrichs, Galt Barber, Donna Karolchik, and sysadmins Paul Tatarsky and Jorge Garcia. See the Credits page for a detailed list of the organizations and individuals who contributed to this release. Posted on 29 Jul. 2004 - Zebrafish Genome Assembly Zv3 Now Available in Genome Browser The Zv3 Zebrafish genome assembly (UCSC version danRer1) is now available on the UCSC Genome Browser and Blat server. This assembly was produced by The Wellcome Trust Sanger Institute, Hinxton, UK, in collaboration with the Max Planck Institute for Developmental Biology in Tuebingen, Germany, and the Netherlands Institute for Developmental Biology (Hubrecht Laboratory), Utrecht, The Netherlands. The Zv3 assembly consists of 1,459,115,486 bp in 58,339 supercontigs, with a sequence coverage of approximately 5.7X. This zebrafish assembly is the first to be tied to the FPC map: 1,083,447,588 bp (74%) of the sequence were mapped in this way. Please note that this is a preliminary assembly; a high level of misassembly is present due to polymorphisms in the DNA source. For more information about this assembly, see the Sanger Institute's Danio rerio Sequencing Project web page. UCSC plans to release the Zv4 version of the zebrafish assembly on the Genome Browser in Fall '04. Downloads of the Zebrafish data and annotations can be obtained from the UCSC FTP site or Downloads page. The danRer1 annotation tracks were generated by UCSC and collaborators worldwide. See the Credits page for a detailed list of the organizations and individuals who contributed to the success of this release. We'd like to thank The Wellcome Trust Sanger Institute and their collaborators for providing this assembly. A special thanks to Yi Zhou, Anthony DiBiase and Leonard Zon from the Children's Hospital in Boston, MA, USA for their collaboration on this release. The UCSC Zebrafish Genome Browser team is Rachel Harte, Heather Trumbower, and Donna Karolchik. Posted on 23 Jul. 2004 - Latest Human Genome Reference Sequence Now in Browser The latest human genome reference sequence (NCBI Build 35, May 2004) is now available as database hg17 in the UCSC Genome Browser and Blat server. This sequence was obtained from NCBI and was produced by the International Human Genome Sequencing Consortium. Bulk downloads of the data are available via FTP at ftp://hgdownload.cse.ucsc.edu/goldenPath/hg17 or through the Downloads link on this page. We recommend that you use FTP rather than HTML for the download of large or multiple files. We'd like to thank NCBI and the International Human Genome Sequencing Consortium for furnishing the data, and the UCSC team members who contributed to this release: Hiram Clawson, Terry Furey, Heather Trumbower, Robert Kuhn, Donna Karolchik, Kate Rosenbloom, Angie Hinrichs, Rachel Harte, Jim Kent and our sysadmin team Patrick Gavin, Jorge Garcia, and Paul Tatarsky. Posted on 23 Jul. 2004 - D. yakuba Added to Genome Browser The UCSC Genome Bioinformatics Group has released a Genome Browser and Blat server on a second species of fruitfly, D. yakuba. The April 2004 Release 1.0 of this genome (UCSC version droYak1) was sequenced and assembled by the Genome Sequencing Center, Washington University (WUSTL) School of Medicine in St. Louis. D. yakuba is closely related to the model organism, D. melanogaster, with which it shared a common ancestor approximately 10 million years ago. The D. yakuba genome is largely alignable to the D. melanogaster genome, but differs sufficiently to offer an interesting study of sequence divergence between the two species. D. yakuba occupies a critical intermediate position among several Drosophila species that will facilitate evolutionary studies among the fruitflies. For information about the D. yakuba assembly and statistics, see the WUSTL Genome Sequencing Center Drosophila yakuba web page. Downloads of the droYak1 data and annotations can be obtained from the UCSC Genome Browser FTP server or Downloads page. The droYak1 annotation tracks were generated by UCSC and collaborators worldwide. Thanks to the Genome Sequencing Center at WUSTL School of Medicine for providing the sequence and assembly of this genome. The UCSC D. yakuba Genome Browser was produced by Angie Hinrichs, Michael Chalup, and Donna Karolchik. See the Credits page for a detailed list of the organizations and individuals who contributed to the success of this release. Posted on 16 Jul. 2004 - Genome Browser Released for Mouse Assembly NCBI Build 33 The latest mouse assembly -- Build 33 from NCBI (UCSC version mm5) -- is now available via the UCSC Genome Browser and Blat server. This assembly includes approximately 2.6 gigabases of sequence. Chromosome 11 is finished in Build 33; the Sanger Institute has provided a corresponding agp file. The whole genome N50 for this assembly is 22.3 Mb, in comparison to 17.7 Mb for the previous build. Please note: the UCSC mm5 assembly contains only the reference strain C57BL/6J. This assembly is a composite version in which phase 3 High Throughput Genome Sequence (HTGS) was merged with the Mouse Genome Sequencing Consortium v3 Whole Genome Shotgun Assembly (MGSCv3). The assembly was performed by NCBI using a "combined" tiling path that was created automatically for the most part, but was manually curated in places. This facilitated the placement of finished sequence in the context of the MGSCv3 assembly. Draft sequence was not included in this build: the slight increase in coverage gained by using this would have been offset by the increase in build errors. More information about Build 33 will be available soon in the NCBI assembly notes and Build 33 statistics. The mm5 sequence and annotation data may be downloaded from the Genome Browser FTP server or Downloads web page. The mm5 annotation tracks were generated by UCSC and collaborators worldwide. We'd like to thank Deanna Church, Richa Agrawala, and the Mouse Genome Sequencing Consortium for this assembly. We'd also like to acknowledge the work of the UCSC mm5 team: Fan Hsu, Hiram Clawson, Angie Hinrichs, Heather Trumbower, Mark Diekhans, Donna Karolchik and our systems administrators Jorge Garcia, Patrick Gavin and Paul Tatarsky. Posted on 15 Jul. 2004 - C. intestinalis v1.0 Released in Genome Browser The v1.0 C. intestinalis draft assembly from the US DOE Joint Genome Institute is now available for study using the UCSC Genome Browser and Blat server (UCSC database ci1). The whole genome shotgun assembly was constructed with the JGI assembler (JAZZ) paired-end sequencing reads at a coverage of 8.2X. The draft contains 116.7 million bp of nonrepetitive sequence in 2,501 scaffolds greater than 3 kb. 60 Mbp of this has been assembled into 117 scaffolds longer than 190 Kbp, and 85% of the assembly (104.1 Mbp) is found in 905 scaffolds longer than 20 kb. The assembly, gene modeling and analysis were performed at the JGI. For more information about the ci1 assembly, see the JGI C. intestinalis project page. Additional information and an analysis of the euchromatic regions of this genome may be found in Dehal et al., The Draft Genome of Ciona intestinalis: Insights into Chordate and Vertebrate Origins. Science. 2002 Dec 13;298(5601):2157-67. Bulk downloads of the sequence and annotation data are available via the Genome Browser FTP server or Downloads page. The ci1 annotation tracks were generated by UCSC and collaborators worldwide. See the Credits page for a detailed list of the organizations and individuals who contributed to this release. Many thanks to the JGI and their collaborators for providing the v1.0 sequence and annotations. The ci1 Genome Browser was produced by Brian Raney, Galt Barber, Heather Trumbower, Robert Kuhn, Donna Karolchik and the Genome Browser sysadmin team - Patrick Gavin, Jorge Garcia, and Paul Tatarsky. We'd also like to thank Tom Pringle for his technical input and Mark Diekhans for his work on the incremental updates for this release. Posted on 14 Jul. 2004 - Genome Browser Released for Dog Draft Assembly v1.0 UCSC has released a Genome Browser and Blat server on the July 2004 v1.0 dog genome sequenced and assembled by the Broad Institute of MIT and Harvard and Agencourt Bioscience. The whole genome shotgun (WGS) sequence is based on 7.6X coverage of the dog genome, assuming a WGS assembly size of 2.4 Gb. The assembly has an N50 contig length of 123 kb and an N50 supercontig length of 41.6 Mb. The dog genome, which contains approximately 2.5 billion base pairs, is similar in size to the genomes of humans and other mammals. The boxer breed was selected for the initial sequencing effort, based on the lower variation rate in its genome relative to other breeds. In addition to the boxer, samples from nine other dog breeds, four wolves and a coyote are being used to generate an initial set of single nucleotide polymorphisms (SNPs) to facilitate disease studies. The SNPs should be available soon from dbSNP. For more information about the dog draft assembly, see the NHGRI press release. The dog sequence and annotation data can be downloaded from the UCSC Genome Browser FTP server or downloads page. These data have specific conditions for use. Many thanks to the Broad Institute of MIT and Harvard, NHGRI, Agencourt Bioscience, Children's Hospital Oakland Research Institute, Centre National de la Recherche Scientifique, North Carolina State University, and Fred Hutchinson Cancer Research Center for their contributions to the sequencing, assembly, and mapping efforts. The initial canFam1 annotation track set, generated by the UCSC Genome Bioinformatics Group, will soon be supplemented by annotations from collaborators worldwide. See the credits page for a detailed list of the organizations and individuals who contributed to the success of this release. Posted on 24 Jun. 2004 - ENCODE Project Featured in Genome Browser We'd like to announce the release of UCSC Genome Browser features tailored to the ENCODE project community, including an ENCODE-specific page to highlight the ENCODE contributors and their work, guidelines for data submission, and a list of specific links to ENCODE regions in the Genome Browser. The initial resources include sequences for the current human assemblies (hg16, hg15, hg13, and hg12), sequence of the comparative species from NISC, tools for coordinate conversion between human assemblies, format descriptions for data submission, and contact information for help with submitting annotation data and analyses. Bulk downloads of the sequence and annotations may be obtained from the ENCODE Project Downloads page. We'd like to thank NHGRI for their support of this project and the various contributors of annotations and analyses. Posted on 10 Jun. 2004 - Genome Browser Training Workshop - Boston, MA The UCSC Bioinformatics Group announces a seminar and hands-on workshop on the UCSC Genome Browser, presented by OpenHelix, a bioinformatics training, software testing and consulting company. This introductory session is geared towards anyone with a basic knowledge of genomic and biological concepts who is interested in learning how to use the UCSC Genome Browser. No programming experience is required. The seminar will cover the topics necessary to learn how to effectively use the browser tool set, including basic Genome Browser functionality, searching and BLAT use, Table Browser use, creating and using custom annotation tracks, and an introduction to the Gene Sorter. The lecture will be accompanied by hands-on computer exercises conducted directly on the Genome Browser web site. The three-hour course will be held at Tufts University School of Medicine, 145 Harrison Street, Boston, MA, on Tuesday, August 10th. Two sessions will be offered: 1 - 4 p.m. or 6 - 9 p.m. For registration information, visit the OpenHelix website or call 1-888-861-5051. Academic, student, and early registration discounts are available. Posted on 28 May 2004 - UCSC Family Browser Name Changed to UCSC Gene Sorter What's in a name? In an effort to clarify the role of the UCSC Family Browser, we have changed its name to the UCSC Gene Sorter. We think this name better describes this tool, which lets the user collect information on groups of genes that may be related in many different ways. The Gene Sorter provides a wealth of information on gene expression, protein homology (both within and across species), GO terms, and Pfam domains, cross links to many other databases, and much more. If you haven't already tried this tool, we encourage you to give it a spin. You'll find it at http://genome.ucsc.edu/cgi-bin/hgNear, or click the "Gene Sorter" link on any Genome Browser menu bar. Posted on 27 May 2004 - New Genome Browser Downloads Server As a follow-up to last week's FTP site switch, we are changing the location of the UCSC Genome Browser downloads site to http://hgdownload.cse.ucsc.edu/. All downloadable files currently located in http://genome.ucsc.edu/goldenPath will be moved to the new server. Please make a note of the new URL and update any references to it. Users accessing downloads through the Genome Browser Downloads page will be redirected automatically to the new location. Posted on 19 May 2004 - New Genome Browser FTP Server We have changed the URL for the UCSC Genome Browser ftp site to ftp://hgdownload.cse.ucsc.edu/. This replaces the old URL of ftp://genome.ucsc.edu/. The old URL will be disabled within a few days. Please make a note of the new URL and update any references to it. Posted on 11 May 2004 - C. elegans WS120 Added to Genome Browser UCSC has released a Genome Browser and Blat server on an updated version of the C. elegans genome. The March 2004 assembly -- UCSC version ce2 -- is based on sequence version WS120 deposited into WormBase as of 1 March 2004. This assembly has a finishing error rate of 1:10,000. The ce2 sequence and annotation data may be downloaded from the Genome Browser FTP server or Downloads web page. The ce2 annotation tracks were generated by UCSC and collaborators worldwide. We'd like to thank the Genome Sequencing Center at Washington University in St. Louis and the Sanger Institute for their collaborative work in sequencing the C. elegans genome. Many thanks to the WormBase consortium for making the worm sequence publicly available. We'd also like to acknowledge the UCSC team who contributed to this release: Rachel Harte (lead engineer), Hiram Clawson (WABA and miRNA annotations), Mike Chalup (QA), Galt Barber (QA), Heather Trumbower (QA), and Donna Karolchik (documentation). Posted on 22 Apr. 2004 - Mouse Genome Assembly Added to Proteome Browser Proteome Browser functionality is now available on the Oct. 2003 mouse genome assembly (mm4). Protein information may be viewed for most genes in the Known Genes track by clicking the Proteome Browser link on the gene's details page. For more information on the UCSC Proteome Browser, see the news release dated 10 March 2004. In conjunction with this release, the Known Genes and Gene Family Browser protein data have been updated to the Swiss-Prot version dated 15 March 2004. Posted on 16 Apr. 2004 - Genome Browser Training - Silicon Valley Area The UCSC Bioinformatics Group announces a seminar and hands-on workshop on the UCSC Genome Browser, presented by OpenHelix, a bioinformatics training, software testing and consulting company. This introductory session is geared towards industry and academic biologists engaged in genomics research. No programming experience is required. The seminar will cover the topics necessary to learn how to effectively use the browser tool set, including basic Genome Browser functionality, searching and BLAT use, Table Browser use, creating and using Custom Tracks, and an introduction to the Family Browser. The lecture will be accompanied by hands-on computer exercises conducted directly on the Genome Browser web site. The three-hour course will be held at the UCSC Extension Campus computer lab in Cupertino, CA on Thursday, May 6th 6-9 p.m. For pricing information or to reserve a seat in the class, visit the OpenHelix web site or call 1-888-861-5051. Pre-registration is required. Academic, student, and early registration discounts are available. Posted on 12 Apr. 2004 - GNF Gene Expression Atlas 2 Data Now Available Expression data from the GNF Gene Expression Atlas 2 are now available on the July 2003 human genome assembly on the UCSC web site. The data may be viewed graphically in the Family Browser or via the GNF Atlas 2 track in the Genome Browser. The track data contain 2 replicates each of 61 mouse tissues and 79 human tissues run over Affymetrix microarrays. We'd like to thank the Genomics Institute of the Novartis Research Foundation (GNF) for providing the expression data underlying the browser displays. More information on the data will be available in the paper Su et al. "A gene atlas of the mouse and human protein-encoding transcriptomes" (in press - PNAS). Posted on 10 Mar. 2004 - Announcing the UCSC Proteome Browser We are proud to announce a new addition to the UCSC family of genome browsing and analysis tools. The UCSC Proteome Browser presents a rich set of useful protein properties as well as links to several protein and genomic data sources on the Web. For the first time, Genome Browser users can have both the genome and proteome worlds at their fingertips simultaneously. The browser is accessible from the Genome Browser via the "Proteome Browser" link on the details page of any gene in the Known Genes track. The initial release is available only on Human Build 34 (hg16); Proteome Browsers for the latest mouse and rat assemblies will follow. For each protein, the browser displays the corresponding genomic exon structure and its amino acid sequence. Several protein property tracks are aligned to the sequence to help a user pinpoint regions of interest. Additional properties are plotted with histograms against genome-wide protein data to highlight significant trends and anomalies. The Proteome Browser is tightly coupled with the UCSC Genome Browser and UCSC Gene Family Browser, allowing easy navigation among the tools. For example, clicking on an exon in the Proteome Browser tracks display brings up the Genome Browser tracks page showing the genomic region of the exon together with a wealth of relevant data. Similarly, clicking on the Proteome Browser's "Family Browser" link displays related gene family information. The v1.0 release of the browser offers a variety of data tracks, including amino acid and DNA sequence, exon boundaries, hydrophobicity, polarity, cysteine and predicted glycosylation sites, Superfamily/SCOP domains, and amino acid anomalies. In addition, the browser includes histograms of several properties on a genome-wide scale: pI, molecular weight, exon count, number of cysteines, InterPro domain counts, hydrophobicity, amino acid frequencies and anomalies. The Proteome Browser also provides links to a variety of external sites containing supplementary information on the protein, including SwissProt, InterPro and Pfam domains, 3-D structures at PDB and UCSF ModBase, and pathway maps of KEGG, BioCarta (CGAP), and BioCyc. We'd like to thank SwissProt for sharing their high quality protein data and the pI calculation algorithm, as well as the other external data sites linked to by the Proteome Browser. We'd also like to acknowledge the hard work of Fan Hsu, lead engineer on the project, and Jim Kent, Tom Pringle, Donna Karolchik, and Robert Kuhn. The project received technical input, review and support from several other members of the UCSC Bioinformatics group. Posted on 1 Mar. 2004 - Chicken Draft Genome Added to Genome Browser We've added the chicken genome to the collection of assemblies available in the UCSC Genome Browser and Blat Server. The Feb. 2004 assembly (UCSC version galGal2) was produced by the Genome Sequencing Center at the Washington University School of Medicine in St. Louis. The source of this sequence was a female inbred Red Jungle Fowl (Gallus gallus), the ancestor of domestic chickens. The chicken genome is the first of the avian genomes to be sequenced. The genome has been sequenced to 6.63X coverage. Approximately 88% of the sequence has been anchored to chromosomes, which include autosomes 1-24, 26-28, and 32, and sex chromosomes W and Z. (In contrast to mammals, the female chicken is heterogametic (ZW) and the male is homogametic (ZZ).) The remaining unanchored contigs have been concatenated into the virtual chromosome "chrUn", separated by gaps of 10,000 bp. The chicken mitochondrial sequence is also available as the virtual chromosome "chrM". Washington University School of Medicine in St. Louis created the physical map for this release. Genetic mapping and linkage analysis were produced through a collaborative effort led by Martien Groenen at Wageningen University in the Netherlands. SNP data based on three strains of domestic chickens will soon be available in GenBank from an international team of scientists led by the Beijing Genomics Institute in China and supported by the Wellcome Trust in Britain. The chicken is considered to be the premier non-mammalian vertebrate model organism. It plays an important role in the research of viruses and cancer, and is a primary model for the study of embryology and development. From an evolutionary standpoint, the chicken's position provides a good intermediate data point between mouse and fugu. Comparative genomics analyses between the chicken and other sequenced organisms should yield valuable information on the evolution of gene order and arrangement, thus improving our understanding of the structure and function of genes. To facilitate comparative genomics studies, alignments of the chicken sequence to the human genome will be available in the Genome Browser later this week. Downloads of the comparative data are currently available through the Downloads page (see below). For more information about the release of the chicken genome assembly, see the NHGRI press release. Additional background on the rationale behind the chicken genome sequencing effort can be found in the sequencing proposal. Bulk downloads of the chicken sequence and annotations may be obtained from the Genome Browser FTP server or Downloads page. These data have specific conditions for use. We'd like to thank the Genome Sequencing Center at the Washington University School of Medicine in St. Louis, Wageningen University, and the Chicken Mapping Consortium for providing these data. The chicken browser annotation tracks were generated by UCSC and collaborators worldwide. See the Credits page for a detailed list of acknowledgements. The UCSC Chicken Genome Browser was produced by Angie Hinrichs, Heather Trumbower, Rachel Harte, and Donna Karolchik. Posted on 23 Feb. 2004 - Chimpanzee Genome Browser Released We are happy to announce the release of a Genome Browser and Blat server for the chimpanzee (Pan troglodytes). The 13 Nov. 2003 Arachne assembly -- labeled Chimp Build 1 Version 1 (UCSC version panTro1) -- was produced by the Chimpanzee Genome Sequencing Consortium. This assembly covers about 95 percent of the genome and is based on 4X sequence coverage. It is composed of 361,782 contigs with an N50 length of 15.7 kb, and 37,849 supercontigs having an N50 length of 8.6 Mb (not including gaps). The total contig length is 2.73 Gb, spanning 3.02 Gb. The DNA donor for this genome assembly, "Clint", is a captive-born West African chimpanzee (Pan troglodytes verus). Background information on the chimp genome sequencing project and the initial news release about the chimp assembly can be found on the NHGRI website. Research has indicated that the human and chimp genomes probably differ by approximately one percent. Because of this close relationship between chimpanzees and humans, the assembly should facilitate comparative analyses of the two genomes that have not been possible with other species that have been sequenced to date. The initial release of the Chimp Browser provides several annotation tracks comparing the chimp and human genomes. More comparative annotations will be added in upcoming weeks. Bulk downloads of the chimp sequence and annotations may be obtained from the Genome Browser FTP server or Downloads page. The complete set of sequence reads is available at the NCBI trace archive. Blat searches on chrUn_random are not supported in the initial release, but will be available soon. We'd like to thank NHGRI, the Eli & Edythe L. Broad Institute at MIT/Harvard, and Washington University at St. Louis School of Medicine for providing this sequence, and LaDeana Hillier, Washington University School of Medicine, and the Broad Institute for their work on the alignments. The chimpanzee browser annotation tracks were generated by UCSC and collaborators worldwide. The UCSC team who worked on this release consisted of Kate Rosenbloom, Jim Kent, Hiram Clawson, Heather Trumbower, Robert Kuhn, Donna Karolchik, and the Genome Browser sysadmin team. Posted on 12 Feb. 2004 - New UCSC-Supported Mirror Site The Genome Browser project now has a UCSC-supported mirror site that may be used during power or network outages on the UCSC campus. The mirror -- which can be found at http://genome.hmgc.mcw.edu/ -- is located at the Medical College of Wisconsin in Milwaukee. The site will be updated regularly by UCSC with the latest data and software to closely replicate the main Genome Browser site at http://genome.ucsc.edu. Please continue to use the UCSC-based site for routine Genome Browser and Blat access. We'd like to thank the Department of Physiology at the Medical College of Wisconsin -- and in particular Jeff Nie and Greg McQuestion -- for their resources and collaboration on this project. We'd also like to acknowledge the hard work of UCSC's Paul Tatarsky, who invested many hours in arranging the collaboration and setting up the mirror. Posted on 16 Jan. 2004 - Eight hg16 Tables Updated We've discovered a handful of hg16 chrN_random_gap and chrN_random_gold tables on our public server that are out of date. We have replaced the following tables with updated versions: chr4_random_gap chr4_random_gold chr8_random_gap chr8_random_gold chrX_random_gap chrX_random_gold chrUn_random_gap chrUn_random_gold Many thanks to Grigoriy Kryukov for discovering this problem. We apologize for any inconvenience this may have caused to our users. Posted on 14 Jan. 2004 - Yeast Genome Browser Released We are proud to add yeast (S. cerevisiae) to our growing list of genome assemblies. The study of brewer's yeast, the most basic eukaryotic model system, has led to important discoveries in a wide variety of areas, including metabolism, centromeres, recombination, cell division control, meiosis and splicing. This assembly (UCSC version sacCer1) is based on sequence dated 1 Oct. 2003 in the Saccharomyces Genome Database (SGD). The sequence, open reading frame (ORF), and gene annotations were downloaded from the site ftp://genome-ftp.stanford.edu/pub/yeast/data_download. The S288C strain was used in this sequencing project. Reference information for each chromosome may be found in the SGD Systematic Sequencing Table. For more information about the yeast genetic and physical maps, see the paper Cherry JM et al. Genetic and physical maps of Saccharomyces cerevisiae. Nature 1997 387(6632 Suppl):67-73. Downloads of the yeast data and annotations may be obtained from the UCSC Genome Browser FTP server or Downloads page. We'd like to thank Stanford University, the SGD, the University of California San Francisco (UCSF), Washington University in St. Louis, and the Eli & Edythe L. Broad Institute at MIT/Harvard for providing the data and annotations for this assembly. We'd also like to acknowledge the UCSC team who worked on this release: Jim Kent, Heather Trumbower, Robert Kuhn, Donna Karolchik, and our sysadmin team. Posted on 10 Dec. 2003 - UCSC Releases Alignments of the Chimp Draft Assembly to Human Genome UCSC has released alignments of the Nov. 2003 chimpanzee draft assembly to the July 2003 human assembly in the Genome Browser. These alignments may be viewed on the Human July 2003 assembly. This release coincides with today's announcement by the National Human Genome Research Institute (NHGRI) of the first draft assembly of the chimpanzee genome. The set of human/chimpanzee alignments consists of a reciprocal best-in-genome net track and a chimp chain track. These alignments were generated using the blastz program developed at Pennsylvania State University and the programs blat, axtChain, chainNet, and netSyntenic developed at UCSC by Jim Kent. Research scientists should find these tracks useful for locating orthologous regions and studying genome rearrangement in the two species. For more information about the alignment tracks, refer to the track description pages. The tables may be downloaded from the Genome Browser FTP server's hg16 database directory. The chimp sequence and alignment data are downloadable from the hg16 human/chimp alignments directory. The chimp sequence used in these alignments was obtained from the 13 Nov. 2003 Arachne assembly. We'd like to thank NHGRI, the Eli & Edythe L. Broad Institute at MIT/Harvard, and Washington University School of Medicine for providing this sequence, and LaDeana Hillier, Washington University School of Medicine, and the Whitehead Institute for their work on the alignments. We'd also like to acknowledge the members of the UCSC team who contributed to the release of these alignments in the Genome Browser: Jim Kent, Kate Rosenbloom, Heather Trumbower, and Donna Karolchik. Posted on 24 Nov. 2003 - Genome Browser Released for Mouse Assembly NCBI Build 32 We have released a Genome Browser and Blat server for the latest mouse genome assembly, NCBI Build 32 (UCSC v. mm4). Build 32 is a composite assembly in which chromosomes were assembled by two slightly different algorithms depending on the available mapping data. Chromosomes 2, 4, 5, 7, 11, 15, 18, 19, X, and Y were assembled using a clone-based tiling path file (TPF) provided by the Mouse Genome Sequencing Consortium (MGSC), with whole genome shotgun sequence used to fill gaps when necessary. The remaining chromosomes were assembled using the MGSCv3 whole genome shotgun assembly as the TPF and merging High Throughput Genomic Sequence (HTGS) as needed. The UCSC mm4 assembly contains only the reference strain C57BL/6J. Build 32 includes 2.6 gigabases of sequence, 1.2 Gb of which is finished. We estimate that 90-96 percent of the mouse genome is present in the assembly. For more information about this version, see the NCBI assembly notes and Build 32 statistics. The mm4 sequence and annotation data may be downloaded from the UCSC Genome Browser downloads page. We'd like to thank the Deanna Church, Richa Agrawala, and the Mouse Genome Sequencing Consortium for this assembly. We'd also like to acknowledge the work of the UCSC mm4 team: Hiram Clawson (lead), Terry Furey, Kate Rosenbloom, Heather Trumbower, Bob Kuhn and Donna Karolchik, and our systems administrators Patrick Gavin, Jorge Garcia and Paul Tatarsky. Posted on 31 Oct. 2003 - D. melanogaster Assembly Added to Genome Browser We have added the Drosophila melanogaster (fruitfly) assembly to the growing collection of genomes available in the UCSC Genome Browser and Blat servers. Release 3.1 (Jan. 2003) of the Drosophila annotated genome sequence was provided by the Berkeley Drosophila Genome Project (BDGP). The 116.8 Mb euchromatic sequence - which is virtually gap-free and of high accuracy - contains six euchromatic chromosome arms represented by 13 scaffolds with a total of 37 sequence gaps. The sequence quality of this release has an estimated error rate of less than one in 100,000 base pairs in the unique portion of the sequence, and less than one in 10,000 base pairs in the repetitive portion. The Release 3.1 sequence was reannotated using the Apollo Genome Annotation and Curation Tool. We also provide data comparing the genome of D. melanogaster with that of D. pseudoobscura. The fruitfly, one of the first organisms to be used in systematic scientific investigations, has been the subject of intensive study in genetics for nearly a century and remains a major model organism in biomedical research, population biology and evolution. We are pleased to add the fruitfly to the roster of assemblies available on our site. Downloads of the Drosophila data and annotations may be obtained from the UCSC Genome Browser ftp site. We'd like to thank BDGP and the Flybase Consortium (Harvard University, University of Cambridge, Indiana University, the University of California, Berkeley and the European Bioinformatics Institute (EBI)) for providing the sequence, assembly, and analysis of this genome. We'd also like to acknowledge the members of the UCSC Genome Bioinformatics group who contributed to this release: Angie Hinrichs (lead engineer), Heather Trumbower, Robert Kuhn, Donna Karolchik, and Jim Kent and the system administrators Jorge Garcia, Patrick Gavin and Paul Tatarsky. Posted on 17 Oct. 2003 - mRNA, RefSeq and EST Data Now Updated Incrementally for Several Assemblies Daily and weekly incremental updates of mRNA, RefSeq, and EST data are now in place for several of the UCSC Genome Browser assemblies. Data sets that are updated incrementally from GenBank include the latest human (hg16), mouse (mm3), rat (rn3), and Fugu (fr1). Others will soon be added to the list. Previously, these tables were updated only when we loaded a new genome assembly into the Genome Browser or made a major revision to a table. By updating the data on a nightly basis, we are able to provide researchers with the most current versions available in GenBank. All new genome assemblies released after this date will incorporate the incremental update technology. Data are updated on the following schedule: - native and xeno mRNA and refSeq tracks - updated daily at 4:30 p.m. Pacific Time (weekdays), early Saturday morning (weekends) - EST data - updated once per week on Saturday morning - downloadable data files - updated weekly on Sunday morning - outdated sequences - removed once per quarter Mirror sites are not required to migrate to an incremental update process, and should not experience problems as a result of this upgrade. Mirror site questions should be addressed to genome-mirror@soe. ucsc.edu. We'd like to acknowledge the hard work of Mark Diekhans in the implementation of this new feature, and thank the QA and sysadmin teams (particularly Paul Tatarsky) for their support in this release. Posted on 17 Oct. 2003 - UCSC Table Browser Enhancements The UCSC Table Browser is an excellent tool for retrieving and searching the data underlying the Genome Browser. We've recently added some new features to the Table Browser to make it even easier to query and download data. Many of our users have requested a batch query utility that will allow them to paste in or upload a list of terms on which to search. You can now do this by clicking the "Item name/accession" button, then uploading a list of search terms by selecting the "Paste in" or "Upload" option. Note that the Paste option supports wildcards, but the Upload option does not. We've also added 2 new lists of searchable tables/tracks. The Browser tracks list contains the names of annotation tracks in the currently selected assembly as they appear in the Genome Browser. This list is useful if you don't know the name of the underlying database table that contains the data in which you're interested. The Custom tracks list contains the names of all custom annotation tables currently loaded into the Genome Browser for the given assembly. This includes tracks that have been created/loaded by the user as well as custom annotations created via the Table Browser. If you have feedback or questions about the Table Browser, please send us email at genome@soe.ucsc.edu. Posted on 29 Sep. 2003 - Introducing the UCSC Gene Family Browser We are pleased to announce the release of the UCSC Gene Family Browser. This major new addition to our website is a useful tool for collecting information on groups of genes that may be related in many different ways. The Browser provides information on gene expression, protein homology (both within and across species), GO terms, and Pfam domains, and cross links to many other databases. To access the Family Browser, click the link on the top menu on this page. The first time you use the Browser, the application will display a brief overview of the tool and information for starting and configuring it. To read a more detailed description of the Browser, see the Family Browser User's Guide. We are always interested in hearing feedback about the tools on our site. If you have comments or questions about the Family Browser, please email us at genome@soe.ucsc.edu. Posted on 23 Sep. 2003 - Fugu Genome Added to Genome Browser We have added the Takifugu rubripes (Japanese pufferfish) assembly to the growing collection of genomes available in the UCSC Genome Browser and Blat servers. The Fugu v.3.0 (Aug. 2002) whole genome shotgun assembly -- which is the fourth vertebrate assembly to be added to the UCSC Genome Browser -- was provided by the US DOE Joint Genome Institute (JGI) as part of the International Fugu Genome Consortium led by JGI and the Singapore Institute of Molecular and Cell Biology (IMCB). This assembly was constructed with the JGI assembler, JAZZ, from paired end sequencing reads produced by JGI and IMCB, at JGI, Myriad Genetics, and Celera Genomics, resulting in a sequence coverage of 5.7X. All reads are plasmid, cosmid, or BAC end sequences, with the predominant coverage derived from 2 Kb insert plasmids. This assembly contains 20,379 scaffolds totaling 319 million base pairs. The largest 679 scaffolds total 160 million base pairs. The Fugu genome was annotated using the Ensembl system by the Fugu informatics group at IMCB. The Fugu, which was one of the first vertebrate genomes to be draft-sequenced after human, serves an important role in the exploration of the human genome. In contrast to other vertebrates that have been sequenced, the intergenic and intron regions of the Fugu are highly compressed and uncluttered with repetitive sequence, resulting in a genome that is unusually compact in size. The Fugu genome has proved useful in gene discovery and the identification and characterization of gene regulatory elements in other genomes. Bulk downloads of the Fugu sequence and annotation data are available via FTP at ftp://hgdownload.cse.ucsc.edu/goldenPath/fr1 or through the Downloads link on the Genome Browser home page. We recommend that FTP be used rather than HTML for the download of large or multiple files. We'd like to thank JGI and the other members of the International Fugu Genome Consortium, including IMCB, the UK Human Genome Mapping Project (Hinxton), the Molecular Sciences Institute (Berkeley) and the Institute for Systems Biology (Seattle), for providing the sequence, assembly, and analysis of this genome. We'd also like to acknowledge the members of the UCSC Genome Bioinformatics group who contributed to this release: Kate Rosenbloom (lead engineer), Heather Trumbower, Robert Kuhn, Donna Karolchik, and Jim Kent. Posted on 13 Aug. 2003 - NISC Comparative Sequencing Program Regions Released in Genome Browser The UCSC Genome Bioinformatics group has released a browser and blat server on the first of more than 100 targeted genomic regions being sequenced in multiple species and analyzed by the NIH Intramural Sequencing Center (NISC) Comparative Sequencing Program sponsored by NHGRI. This release coincides with the publication of the results of the study in the 14 Aug 2003 issue of Nature (Thomas, J.W. et. al. (2003) Comparative analyses of multi-species sequences from targeted genomic regions. Nature 424:788- 793). The browser displays sequence and annotations on a large region containing 10 previously identified genes - including the gene mutated in cystic fibrosis - in 13 vertebrate species. Organisms in the study include human, chimpanzee, baboon, cat, dog, cow, pig, rat, mouse, chicken, zebrafish and two species of pufferfish (Fugu and Tetraodon). The NISC Comparative Sequencing Program data may be accessed by clicking the Browser link on the Genome Browser home page and then selecting the "Zoo" option from the genome list. The research team, led by NHGRI Scientific Director Eric D. Green, included scientists from Pennsylvania State University, University of California Santa Cruz (UCSC), and the University of Washington in Seattle. In the study, the investigators systematically compared the patterns of transposon insertions among the species' sequences. One key result of the analysis was the confirmation of recently proposed mammalian evolutionary trees suggesting that primates are more closely related to rodents than to carnivores or artiodactyls. Another significant outcome was the discovery of a substantial number of previously unidentified non-coding DNA segments that are conserved across a wide range of species. Many of these regions could be identified only through comparisons of sequence from multiple species, demonstrating the importance of studying the genomes of a wide range of organisms as a means for identifying functional elements in the human genome. UCSC built a customized version of the browser to display the target region for this study, allowing scientists to interactively explore the data and predictions generated by this project, contribute data of their own, and track the project as data from additional species are generated. In addition to the browser, the UCSC team also contributed to the analytical portion of the study. Mathieu Blanchette identified the regions that are most highly conserved among species. Adam Siepel performed the phylogenetic analysis of rates of substitution. The UCSC team worked with Arian Smit to obtain definitive evidence that rodents branched off from the common ancestor later than carnivores and artiodactyls. For more information on the NISC study, see the Science Daily press release. Flat files of the assembled sequence and annotations may be obtained from http://www.nisc.nih.gov/data/ or via the Downloads link on the Genome Browser home page. We'd like to thank the NISC Comparative Sequencing Program team for providing the data and comparative analysis for this Genome Browser release. Special thanks go to Elliott Margulies at NHGRI for serving as the main liaison between NHGRI and UCSC, and for contributing several annotation tracks to the browser. We'd also like to acknowledge the efforts of the many faculty, grad students, and staff members of the UCSC Genome Bioinformatics group who contributed to the research effort and browser development for this project. Posted on 8 Aug. 2003 - New Human Genome Reference Sequence Now Available in Genome Browser The latest human genome reference sequence (NCBI Build 34, July 2003) is now available as database hg16 in the UCSC Genome Browser and blat server. There are 2,843,433,602 finished sequenced bases in the ordered and oriented portion of the assembly, which is an increase of 0.4 percent, or approximately 11 Mb, over the Build 33 assembly. Of particular note in this release is the addition of the pseudoautosomal regions of the Y chromosome. This sequence was taken from the corresponding regions in the X chromosome and is an exact duplication of that sequence. Some sequence joins between adjacent clones in this assembly could not be computationally validated because the clones originated from different haplotypes and contained polymorphisms in the overlapping sequence, or the overlap was too small to be to be reliable. In these instances, the sequencing center responsible for the particular chromosome has provided data to support the join in the form of an electronic certificate. The Build 34 certificates may be reviewed here. Bulk downloads of the data are available via FTP at ftp://hgdownload.cse.ucsc.edu/goldenPath/hg16 or through the Downloads link. We recommend that FTP be used rather than HTML for the download of large or multiple files. We'd like to thank NCBI and the International Human Genome Sequencing Consortium for furnishing the data, and the UCSC team members who contributed to this release: Terry Furey, Hiram Clawson, Heather Trumbower, Mark Diekhans, Robert Baertsch, Donna Karolchik, Jim Kent and our sysadmin team Patrick Gavin, Jorge Garcia, and Paul Tatarsky. Posted on 14 Jul. 2003 - Rat Genome v.3.1 Added to Genome Browser The UCSC Genome Bioinformatics Group has released a browser and BLAT server on the v. 3.1 rat genome assembly from the Rat Genome Sequencing Consortium. This assembly (UCSC version rn3, June 2003) was produced by the Atlas group at Baylor Human Genome Sequencing Center (HGSC). This assembly is a minor update to the 3.0 release. Sequence changes affect only chromosomes 7 and X. No additional assembly releases are planned prior to the publication of the rat genome analysis papers. The 3.x assemblies reflect several sequence additions and software improvements over the previous 2.x assemblies, including the sequencing of over 1100 new BACs to cover gaps, an improved marker set from the Medical College of Wisconsin, a new FPC map from the BC Genome Sciences Centre, and improved linking of bactigs. For detailed information and statistics about the 3.x assemblies, see the Baylor HGSC README. Downloads of the rat sequence and annotation data are available at ftp://hgdownload.cse.ucsc.edu/goldenPath/rnJun2003/ or via the Downloads link on this page. These data are made available with specific conditions for use. We'd like to thank the Rat Genome Sequencing Consortium and Baylor HGSC for providing this assembly, collaborators from other institutions who have contributed annotations, and Arian Smit for updating RepeatMasker for this release. We'd also like to acknowledge the contributions of several individuals at UCSC, including Hiram Clawson, Heather Trumbower, Robert Kuhn, Yontao Lu, Terry Furey, Mark Diekhans, Robert Baertsch, Donna Karolchik, Jim Kent, and our sysadmin team Jorge Garcia, Patrick Gavin, and Paul Tatarsky. Posted on 24 Jun. 2003 - Genome Browsers Released for C. elegans and C. briggsae UCSC has just released browsers and blat servers for 2 worms: C. elegans version WS100 (May 2003) and C. briggsae version cb25.agp8 (July 2002). The browsers are based on sequence obtained from WormBase. We are pleased to add the nematodes to the roster of genomes available on our site. C. elegans is a major model organism used for biomedical research, and is the first multicellular animal to have a fully sequenced genome. In contrast, the whole genome shotgun assembly of the C. briggsae genome is estimated to have achieved 98% coverage. Draft chromosome sequences are not available for C. briggsae, due to the lack of dense chromosomal maps that allow assignment of ultracontigs to chromosomal locations. As a result, all data in the C. briggsae browser maps to chrUn. Both worms played a significant role in the early history of the UCSC Genome Browser. The browser code originated with a C script that displayed a splicing diagram for a gene prediction from C. elegans. Tracks for mRNA alignments and for homology with C. briggsae were added, and the tool morphed into the precursor of the Genome Browser, the "Intronerator" (Kent, WJ and Zahler, AM (2000). The intronerator: Exploring introns and alternative splicing in C. elegans. Nucleic Acids Res. 28: 91-93). Downloads of the C. elegans sequence and annotation data are available at ftp://hgdownload.cse.ucsc.edu/goldenPath/ceMay2003/; C. briggsae downloads can be found at ftp://hgdownload.cse.ucsc.edu/goldenPath/cbJul2002/. Both genomes can also be downloaded via the Downloads link on this page. We'd like to thank the Genome Sequencing Center at Washington University in St. Louis and the Sanger Institute for their collaborative work in sequencing the C. elegans and C. briggsae genomes. Many thanks to the WormBase consortium for making the worm sequence publicly available. We'd also like to acknowledge several UCSC people who contributed to this release: Hiram Clawson (browser and annotation tracks engineering), Jim Kent (WABA and chaining/netting), Al Zahler (WABA), Heather Trumbower (QA and project management), and Donna Karolchik (project management and documentation). Posted on 23 Jun. 2003 - Genome Browser UI Changes You may notice that we've removed the Genome pulldown menu and genome assembly information from our home page. Genome-specific information and links, as well as genome selection, are now available on the gateway pages for our tools. To open up a gateway page, simply click the Browser, Blat, or Tables link in the left sidebar. Posted on 23 May 2003 - SARS Coronavirus TOR2 Draft Assembly Available [NOTE: The SARS assembly is no longer available on our public site, but may be accessed on our test server, genome-test.cse.ucsc.edu.] Today we'd like to announce the release of a genome browser and BLAT server for the SARS coronavirus TOR2 draft assembly. The browser - which is based on sequence deposited into GenBank as of 14 April 2003 - provides seven annotations showing gene predictions, locations of putative proteins, and viral mRNA and protein alignments. Of particular note are the protein structure analysis and predictions, determined by using the Sequence Alignment and Modeling (SAM) T02 tool. This browser marks a departure from our usual collection of vertebrate genomes. Its inception was inspired by one of our engineers - Angie Hinrichs - who was vacationing in New Zealand when the SARs draft assembly was initially released. Struck by the impact of SARS in that part of the world, she downloaded the sequence and built the initial tracks from a terminal at an Internet cafe! The rest of the team joined in on the grassroots effort, generating the additional annotations and SAM T02 protein analyses and predictions. Victor Solovyev chimed in with Fgenesv+ gene predictions from Softberry Inc. UCSC does not intend to provide a comprehensive collection of viral genomes in the future, but will maintain this browser as long as scientific and public interest in SARS persists. Downloads of the annotation data are available at ftp://hgdownload.cse.ucsc.edu/goldenPath/scApr2003/database or via the Downloads link on this page. We'd like to thank everyone who worked on this release, including Angie Hinrichs, Robert Baertsch, Fan Hsu, Matt Schwartz, Heather Trumbower, Jim Kent, Kevin Karplus, Donna Karolchik, Brian Raney, Hiram Clawson, Kate Rosenbloom, Victor Solovyev, and our extremely dedicated systems administrators Paul Tatarsky, Patrick Gavin, and Jorge Garcia. Posted on 21 Apr. 2003 - Chromosome 8 Data Corrected for April 2003 Human Assembly The file that we originally used to build the agp files for the April 2003 human release (Build 33) erroneously contained 2 contigs on chromosome 8 that were listed twice: NT_078037, NT_008183. We've received a corrected version and have updated the following files on our website: contigAgp.zip, chromAgp.zip, liftAll.zip. You can obtain the newer versions of these files from our ftp site at ftp://hgdownload.cse.ucsc.edu/goldenPath/10april2003/bigZips/. Posted on 14 Apr. 2003 - Human Genome Project Successfully Completed! The International Human Genome Sequencing Consortium today announced the successful completion of the Human Genome Project. The most significant outcome of this project is the reference sequence of the human genome. The sequencing of the 3 billion letters of DNA in the human genome - which many consider to be one of the most ambitious scientific undertakings in history - was completed 2 years ahead of schedule and at substantially less cost than original estimates. The reference sequence will serve as a new foundation for research in the fields of medicine and human biology. In conjunction with this announcement, the UCSC Genome Bioinformatics group is proud to release a genome browser and BLAT server on the reference sequence (NCBI Build 33), along with bulk downloads of the sequence and annotation data. The initial browser provides a preliminary set of annotations that will be expanded in coming weeks. Bulk downloads of the data are available via FTP at ftp://hgdownload.cse.ucsc.edu/goldenPath/10april2003 or through the Downloads link on this page. We recommend that FTP be used rather than HTML for the download of large or multiple files. The reference sequence covers about 99 percent of the human genome's gene-containing regions, and has been sequenced to an accuracy of 99.99 percent. The missing portions are essentially contained in less than 400 defined gaps that represent DNA regions with unusual structures that can't be reliably sequenced using current technology. The average DNA letter now lies within a stretch of approximately 27,332,000 base pairs of uninterrupted sequence! Chromosomal sequences for this release were assembled by the International Human Genome Sequencing Consortium sequencing centers and verified by NCBI and UCSC. In some cases, sequence joins between adjacent clones could not be computationally validated, e.g. due to polymorphisms in the overlapping sequence. In situations like this, supporting evidence for the join has been provided by the sequencing center responsible for that particular chromosome. The Non-standard Join Certificates table displays this information. The annotations on the UCSC website have been provided by UCSC and collaborators worldwide. See the Credits page for a detailed list of organizations and individuals who contributed to the success of this release. We'd like to congratulate the many people worldwide who have worked on the Human Genome Project for this landmark achievement. We'd also like to acknowledge the UCSC Genome Browser project team who worked many long hours to ensure that the genome browser and sequence data were released on time for this announcement: David Haussler, Jim Kent, Terry Furey, Matt Schwartz, Heather Trumbower, Angie Hinrichs, Fan Hsu, Donna Karolchik, Jorge Garcia, Patrick Gavin, Chuck Sugnet, Yontao Lu, Mark Diekhans, Ryan Weber, Robert Baertsch, Krishna Roskin, and the many other students in the UCSC Genome Bioinformatics group. Posted on 2 Apr. 2003 - Human Assembly hg10 and Mouse Assembly mm1 Archived The Dec. 2001 Human assembly (hg10) and the Nov. 2001 Mouse assembly (mm1) have been moved to the archives. They are no longer accessible from the main browser, but instead can be found by clicking the Archives link on this page. Posted on 26 Mar. 2003 - New Rat Assembly Released in Genome Browser We've added an updated rat assembly to our site: Rat Jan 2003 (rn2). This corresponds to the Version 2.1 Jan 2003 Update of the rat genome assembly, produced by the Atlas group at Baylor HGSC as part of the Rat Genome Sequencing Consortium. This update corrects duplications that were assembly artifacts in the previous version and improves the linking of bactigs to create larger "ultrabactigs". Compared with the previous rat assembly, sequence mapped to specific chromosomal coordinates is reduced by about 1.6 percent. Loosely mapped and unmapped sequence is reduced by 17 percent. For more details and statistics on the Jan 2003 assembly, see the Baylor HGSC README for this release. UCSC has released a Genome Browser and BLAT server for this assembly update. The initial browser contains 16 annotation tracks, with more to follow in coming weeks. Sequence downloads are currently available at ftp://hgdownload.cse.ucsc.edu/goldenPath/rnJan2003/ or via the Downloads link on this page. A complete set of database downloads will be available at the beginning of next week. This data contains specific conditions for use. Thanks to the Atlas group at Baylor HGSC, the Rat Genome Sequencing Consortium, the UCSC Genome Bioinformatics group, and contributors worldwide for making this release available. Posted on 13 Mar. 2003 - Updated Mouse Genome Assembly Now Available We're happy to announce an update to the mouse genome sequence. This new version (Mouse Feb. 2003) includes 705 megabases of finished sequence, compared to 96 megabases of finished sequence in the previous assembly. Many people in the Mouse Genome Sequencing Consortium contributed to this update. The Sanger Institute in particular contributed a large amount of finished sequence. Richa Agarwala, Deanna Church, and coworkers at NCBI layered the finished clones on top of the Arachne whole genome shotgun assembly. Arian Smit constructed a new RepeatMasker library. UCSC has released a Genome Browser and BLAT server for the Feb. 2003 Mouse genome. The initial browser contains 14 annotation tracks, with more to follow in coming weeks. Sequence downloads are currently available at ftp://hgdownload.cse.ucsc.edu/goldenPath/mmFeb2003/ or via the Downloads link on this page. Database downloads will be available at the beginning of next week. Thanks to everybody at UCSC and around the world that contributed to the success of this release! Posted on 5 Feb. 2003 - Enhanced Version of Genome Browser Released We're proud to announce the release of version 17 of the UCSC Genome Browser. This version contains powerful new features, numerous improvements to the annotation track display, additional annotation tracks, and a number of bug fixes. In this release cycle, we've also introduced an enhanced QA process that formalizes our testing and verification of the Genome Browser software and the data displayed in the browser. New functionality in v.17: -- Numerous enhancements to the table browser that allow the user to conduct more complex and specific searches. New features include support for intersections of tracks, a new summary statistics output format, and the ability to output query results as a custom annotation track that can be viewed in the Genome Browser. The new Table Browser User's Guide contains a detailed description of the new features and provides a wealth of information and examples for conducting various types of searches on the database tables. -- Two new display modes available for most annotation tracks: pack and squish modes. In pack mode display, annotation track features are f ully displayed, but more than one feature may be displayed on the same line. This greatly reduces the amount of display space needed by a track when a user wishes to view a large number of individual features at one time. Squish mode is similar to pack mode, but displays features at 50% height and without labels. This mode is particularly useful for viewing tracks in which a large number of features align to the same section of a chromosome, e.g. EST tracks. -- Functional groupings of annotation track controls. This makes it much easier to find a particular item in the track control list and gives a better visual overview of the annotations available in a particular category, e.g. comparative genomics tracks or gene prediction tracks. -- A mechanism for saving the annotation tracks image in postscript or PDF format. This much requested feature enables Genome Browser users to print an image at high resolution, edit it with a drawing program, or display it in a postscript or PDF viewer. -- A collection of custom annotation tracks supplied by Genome Browser users and members of the UCSC Genome Bioinformatics lab. Additional contributions to this collection are welcome! Contact genome@soe.ucsc.edu if you have an annotation you'd like to share. New annotation tracks in v.17: -- a new Known Genes track (Human Builds 30 & 31, Feb 2002 Mouse, Nov 2002 Rat) that shows known protein coding genes based on proteins from SWISS-PROT, TrEMBL, and TrEMBL-NEW and their corresponding mRNAs from Genbank. Features within the track are color-coded according to origin and review status. -- a new Superfamily track (Human Build 30, Feb 2002 Mouse) that shows proteins having homologs with known structures or functions. Each entry in the track shows the coding region of a gene (based on Ensembl gene prediction). The feature label consists of the names of all known protein domains coded by the gene, and usually contains structural and/or function descriptions that provide valuable information for getting a quick grasp of the biological significance for the gene. We have also released several additional annotation tracks on the latest human and rat assemblies in the past month. Bug fixes in v.17: -- Approximately 40 bugs (mostly minor problems) have been fixed in this version. To take full advantage of the new display features in this release, we recommend that you reset your browser to the new default settings. NOTE: you may not want to reset your browser if you have customized settings that you wish to preserve. You can reset your browser by clicking the "Click here to reset" link on the Browser Gateway page. We hope this new release facilitates your work with the UCSC Genome Browser. If you have any questions or comments about the new release, send email to genome@soe.ucsc.edu. Posted on 23 Dec. 2002 - Human Genome Assembly Build 31 Released in Genome Browser We're pleased to announce the release of the latest human genome assembly, Build 31 (UCSC version hg13). This assembly was produced at NCBI based on sequence information submitted into GenBank as of Nov. 14, 2002. Release notes for this assembly are available from the NCBI web site. Because UCSC now obtains its assembly directly from NCBI, the UCSC Build 31 data is identical to that of NCBI and Ensembl. Build 31 is an excellent high-quality assembly that shows a remarkable amount of progress toward the milestone of finishing the human genome. Greater than 95% of the euchromatic region of the genome is now complete, with more than 90% of the sequence in a finished state. The number of clone contig gaps has decreased by one third from the previous assembly, and the overall number of sequenced contigs has been reduced by one half. Seven chromosomes are considered to be in a finished state: 6, 7, 13, 20, 21, 22, and Y. The initial release of the Build 31 Genome Browser contains 25 annotation tracks, with several more to follow in the upcoming weeks. Bulk downloads of the data are available from our FTP site at ftp://hgdownload.cse.ucsc.edu/goldenPath/14nov2002 or via the Downloads link on this page. UCSC has generated a set of high-level comparisons of the Build 31 draft sequence against various types of information (STS maps, BAC end pairs, and clone overlaps). This information, as well as statistics for Build 31, is accessible from the Chromosome Reports, Genome Map Plots, and Summary Statistics links in the "Technical Information about the Assembled Sequence" section below. We'd like to thank NCBI as well as all the people who collaborated on the data and annotations for this release. Posted on 6 Dec. 2002 - Rat Genome Assembly Now Available in Genome Browser We're pleased to announce the release of a UCSC Genome Browser on the Nov. 2002 rat assembly produced by the Baylor College of Medicine Rat Genome Sequencing Center and the Rat Genome Sequencing Consortium. The sequence was assembled using a hybrid approach that combines the clone by clone and whole genome shotgun methods. A new software program - ATLAS - was developed for this effort. The assembly process resulted in a 6.5-fold coverage of the rat genome, which is estimated to be approximately 2.8 Gigabases in size. Downloads of the rat data and annotations are available through our ftp site at ftp://genome-archive.cse.ucsc.edu/goldenPath/rnNov2002 or via the archived downloads link. This data contains specific conditions for use. The sequence is also available from the Rat Genome Project website for the Human Genome Sequencing Center at Baylor College of Medicine or from GenBank. We'd like to thank the Baylor team and the Rat Genome Sequencing Consortium for their collaboration on this project. See the Credits page for a complete list of acknowledgments.. For more information on the rat genome, the assembly process, and the Rat Genome Sequencing Consortium, refer to the website for the Human Genome Sequencing Center at Baylor College of Medicine. Posted on 5 Dec. 2002 - Mouse Genome Browser Released The International Mouse Genome Sequencing Consortium has announced the publication of a high-quality draft sequence of the mouse genome, together with a comparative analysis of the mouse and human genomes. The results from this analysis can be found in the Mouse Genome Browser on this website. The paper appears in the Dec. 5 issue of the journal Nature at http://www.nature.com/nature/mousegenome/. The co-author list includes several members of the UCSC Genome Bioinformatics Group: CBSE Director David Haussler, Research Scientist Jim Kent and research team members Robert Baertsch, Mark Diekhans, Terrence Furey, Angie Hinrichs, Fan Hsu, Donna Karolchik, Krishna Roskin, Matt Schwartz, Charles Sugnet and Ryan Weber. Posted on 29 Oct. 2002 - Additional Data Downloads Available for Human Assembly June 2002 We've added several new directories of downloadable data to the 28 June 2002 human genome assembly. These directories contain mouse/human alignments of the June 2002 human assembly vs. the Feb. 2002 mouse assembly. You can access these directories from our archived downloads link or or via our ftp site at ftp://genome-archive.cse.ucsc.edu/goldenPath/28jun2002/vsMm2/. Within the main directory vsMm2 are 3 subdirectories that contain all the alignments (axtAll), alignments filtered to provide only the best alignment for any given region of the human genome (axtBest), and a relatively stringent subset of the axtBest alignments (axtTight). For more information about the format of the alignment files and the methods used to generate the alignments, consult the README.txt file in the vsMm2 directory. Posted on 18 Oct. 2002 - Enhancements in v16 Genome Browser We've rolled out a new version of the Genome Browser - v.16. In addition to several bug fixes, this release contains some interesting new features. The Table Browser has undergone major enhancements. Users can now restrict their queries by specifying a value or range for any of the fields in a table, and by selecting which fields should be displayed in the output. The Table Browser also provides the ability to do a free-form SQL query on a table and supports several new output formats. We've extended the capabilities of the DNA retrieval functionality in the Genome Browser and the Table Browser. The new mechanism offers the user several options for configuring the amount and type of sequence region that is retrieved, and options for formatting the sequence output. The retrieval options vary based on the type of table selected. The Genome Browser's gene prediction tracks now offer a Comparative Sequence link in addition to the predicted protein, mRNA sequence, and genomic sequence links. The Comparative Sequence feature displays annotated codons and translated protein for the region in alignment to another species. We've recently added a few new tracks/tables to the hg12 and mm2 Browsers. On the latest human assembly (hg12), we now have Chimp Blat and Chimp BAC tracks provided by Ingo Ebersberger, Joshua Bacher, and Svante Pääbo at the Max Planck Institute for Evolutionary Anthropology. Jim Kent at UCSC has generated a new annotation - Gene Boundaries - that shows the boundaries of genes and the direction of transcription as deduced from clustering spliced ESTs and mRNAs against the genome. Daryl Thomas of UCSC has also added SNP tracks to both hg12 and the latest mouse assembly (mm2), based on data from the SNP Consortium and NIH. We encourage you to experiment with these new features. Comments, questions, and suggestions are always welcome at genome@soe.ucsc.edu. Posted on 17 Oct. 2002 - Corrections to Mouse Assembly mm2 Repeat-masking We have found errors with the RepeatMasker track on the Feb. '02 mouse assembly (mm2). This problem affects the RepeatMasker track and RepeatMasked DNA obtained via the browser's DNA links. It does not affect data downloaded from the browser's downloads page or ftp site. We have replaced the erroneous data set with a corrected version. If you have questions about how this change may affect your project, email genome@soe.ucsc.edu. Posted on 4 Oct. 2002 - Chromosome 22 Coordinate Differences Between UCSC and NCBI Please note that the coordinate range for a portion of the Build 30 chr22 in the UCSC Genome Browser differs from that of NCBI and the Sanger Centre. The latter version contains a 100K bp gap inserted into chr22 just after the centromere. This modification was made after UCSC released the Build 30 assembly in the Genome Browser. All of the chr22 annotations displayed by the UCSC browser are correctly positioned relative to one another. However the coordinates of all features past the centromere will be 100K less than those of NCBI and Sanger. The Ensembl Genome Browser is consistent with the UCSC browser. Posted on 19 Sep. 2002 - Release of Human/Mouse Evolutionary Conservation Score Annotation We're pleased to announce the release of the Mouse Cons (Human/Mouse Evolutionary Conservation Score) annotation track for the June 2002 human genome assembly. This track allows a user to interactively explore conservation between the human and mouse genomes and identify highly conserved regions. Highest levels of conservation are typically seen over coding exons. High levels of conservation are also frequently associated with noncoding RNA, promoters, other regulatory elements, and pseudogenes. The Mouse Cons annotation is displayed using a new type of Genome Browser graphical track that plots a continuous function along a chromosome. The conservation levels are calculated over 50bp windows in the human genome that have at least 15 bp aligned to mouse. The score for a window reflects the probability that the level of observed conservation in that 50bp region would occur by chance under neutral evolution. This information is given on a logarithmic scale and displays in the track as "mountain ranges". Details pages associated with the individual peaks in the track provide access to the base level alignments for the whole region and for the individual 50bp windows. The team that produced this track includes Ryan Weber, Krishna Roskin, Mark Diekhans, Jim Kent, Scott Schwartz, and Webb Miller. Posted on 12 Sep. 2002 - "User's Guide to the Human Genome" Features UCSC Genome Browser Nature Genetics has just published User's Guide to the Human Genome, a hands-on tutorial for using genome browsers as web tools for browsing and analyzing data from the Human Genome Project and other sequencing efforts. The 3 browsers featured in the tutorial include the UCSC Genome Browser, NCBI's Map Viewer, and the Ensembl Genome Browser. The guide is organized around a collection of step-by-step solutions to 13 typical research questions, and serves as a nice supplement to the documentation materials available on the UCSC Genome Browser web site. The guide is accessible as a link off the Nature Genetics home page at http://www.nature.com.ng. Posted on 12 Sep. 2002 - Correction to Human Assembly hg12 Chromosome Bands Annotation We've corrected a problem with the Human June 2002 (hg12) cytoBand annotation track that affected chromosome Y. The clones on this chromosome were erroneously pushed from the q-arm onto the p-arm, creating some confusion. The currently available version of the cytoBand data on this website contains this correction. Posted on 15 Aug. 2002 - Additional Annotations for Human Draft Assembly hg12 Released We've just released several new annotation tracks/tables for the human genome. On the June 2002 assembly, we've added Gene Bounds, UniGene, CpG Islands, Nonhuman mRNA & EST, SNPs, NC160, and GNF Ratio. On the April 2002 assembly we've added a Fgenesh++ Genes track, and have also updated the RepeatMasker track. The Dec. 2001 release now includes a Sanger 22 track. On the mouse genome, we have 2 new tracks for the Feb. 2002 assembly: TIGR Gene Index and RNA Genes. Posted on 6 Aug. 2002 - Error with Six Chromosome 3 Contigs in Human Assembly hg12 We have fixed an error with six of the chr3 contigs in the bigZips/contigAgp.zip file. The following .agp files were corrected: NT_005684.agp, NT_005663.agp, NT_022554.agp, NT_022459.agp, NT_006031.agp, and NT_022419.agp. The chr3.agp file in bigZips/chromAgp.zip was also modified. This change does not affect the .gl files, the .fa files, the lift files, or the annotations. Alignments made on the previous version of chr3 are still good. Updated versions of the contigAgp.zip and chromAgp.zip files were uploaded to our site today. You can download the new versions via ftp at ftp://genome-archive.cse.ucsc.edu/goldenPath/28jun2002 or via the archived downloads link. Posted on 2 Aug. 2002 - New RepeatMasker Track Available for Human Assembly hg12 The problems with the June 2002 Build 30 (hg12) RepeatMasker track have been resolved. The new RepeatMasker track, along with regenerated Fish Blat and Genscan tracks, are now available in the Browser and through our Downloads link. We've also added a few new annotation tracks for the June 2002 release, and will be adding more over the next 2 weeks. The latest Genome Browser has 2 new features. We've added filter functionality to the Table Browser, accessible via the Filter Fields button on the Table Browser main page. Also, some of the Dec. 2001 human genome tracks (eg. RefSeq Genes) now have a Comparative Sequence link from the details page that shows annotated codons and translated protein with alignment to the mouse genome. Posted on 27 Jul. 2002 - Problems with Repeat-masking on Human Assembly hg12 We've experienced some RepeatMasker problems on Build 30 and are rerunning it. This will directly affect the RepeatMasker track and the masking of the fasta files. The Fish Blat and Genscan tracks may also change slightly once we're redone this. The EST, mRNA, and RefSeq tracks should not be affected. We will also post a new RepeatMasker track for Build 29 (see news item below) as soon as the Build 30 tracks are completed. We apologize for any rework this may cause. Posted on 26 Jul. 2002 - Bulk Data Downloads Now Available for Human Assembly hg12 Bulk downloads of the June 2002 Build 30 human genome assembly (hg12) are now available from ftp://genome-archive.cse.ucsc.edu/goldenPath/28jun2002. You can also access the data via the archived downloads link. This initial release of the annotation database download contains a limited set of tables. Additional files will be available for download next week. Posted on 24 Jul. 2002 - Human Assembly hg12 Blat Server Available The BLAT server and the coordinates conversion feature for human genome assembly Build 30 (hg12) are now functional. Posted on 23 Jul. 2002 - Pre-release of Human Draft Assembly Build 30 in Genome Browser We're pleased to announce the pre-release of a browser for human genome assembly Build 30 from NCBI (UCSC version hg12). This assembly was produced at NCBI based on sequence information submitted into GenBank as of June 28, 2002. Build 30 release notes and statistics will soon be available from the NCBI web site. Build 30 is an excellent high-quality assembly. It contains nearly 87% finished sequence, and 94%-97% coverage. The sequence coverage of this build is much higher than in previous releases, and there is a high level of correspondence between the sequence and the map. Currently, the human genome project appears to be on track to achieve the goal of finishing at least 95% of the human genome (using Bermuda standards) by April 2003. UCSC has generated a set of high-level comparisons of the Build 30 draft sequence against various types of information (STS maps, BAC end pairs, and clone overlaps), accessible from the Chromosome Reports and Genome Map Plots links in the "Technical Information about the Assembled Sequence" section below. A Blat server for Build 30 is not yet available, but should be accessible from this site later this week. Data for the mitochondrial genome and several more annotation tracks will be posted for this release as they become available. Bulk downloads of the hg12 data should be available from this site in a few days. Posted on 9 Jul. 2002 - Repeat-masking Problems on Human Assembly hg11 We've found some problems with the repeat-masking of the Build 29 (hg11) human sequence. We're in the process of replacing the RepeatMasker track, but do not plan to redo the other tracks due to the imminent release of Build 30. Because of this, we advise that you do not use the cross-species tracks for statistical purposes. Posted on 1 Jul. 2002 - New Look for UCSC Genome Bioinformatics Home Page The UCSC Genome Bioinformatics home page is sporting an updated interface to accommodate the growing number of organisms supported by the UCSC Genome Browser, BLAT, and Table Browser. The list of assembly versions accessible through each of these tools can now be found on the tool's Gateway page. To reach the Gateway page, choose an organism from the dropdown list on the left sidebar of this page, then click the Browser, BLAT, or Tables link. New organisms will be added to the list in the months ahead. The UCSC site continues to provide a variety of bulk downloads of a genome assemblies and annotations. The list of downloadable data has been removed from the home page, but is readily available through the Downloads link on the left sidebar. The downloads list can also be accessed directly at http://hgdownload.cse.ucsc.edu/downloads.html or through our ftp site at ftp://hgdownload.cse.ucsc.edu/goldenPath/. Several new annotation tracks have been added to our site in the past couple weeks. The Feb. 2002 mouse assembly now has tracks for BAC End pairs, Fgenesh++ gene predictions, and AltGenie gene predictions based on Affymetrix's Genie gene-finding software. New to the Apr. 2002 human assembly is the GenMapDB Clones track, which shows placements of BAC clones from the GenMapDB database based on BAC end sequencing information and confirmed using STS markers by Vivian Cheung's lab at U. Penn. We've also changed the Known Genes track name to RefSeq Genes in all assemblies. This release also includes an updated User's Guide and more detailed documentation on creating & using custom annotation tracks. Posted on 24 May 2002 - Bulk Data Downloads for Human Assembly hg11 Now Available Bulk downloads of the April 2002 hg11 human genome assembly (NCBI Build 29) are now available from ftp://genome-archive.cse.ucsc.edu/goldenPath/05apr2002. You can also access the data from the Downloads link in the left sidebar. Posted on 22 May 2002 - Human Draft Assembly Build 29 Released in Genome Browser We've just released a browser and BLAT server on the latest Build 29 human genome assembly from NCBI (UCSC version hg11). This assembly is based on sequence information submitted into GenBank as of Apr. 5 2002. As with the Dec. 2001 (hg10) release, this assembly was produced at NCBI rather than at UCSC. Consult NCBI's Build 29 release notes and statistics for more information about this release. This assembly contains nearly 75% finished sequence. Currently, the human genome project appears to be on track to achieve the goal of finishing at least 95% of the human genome (using Bermuda standards) by April 2003. Although the NCBI human genome assembly has been steadily improving over the past year, mapping problems still exist in the current release. Most are small, relatively local rearrangements. Larger scale problems include a rearrangement in the p-arm of Chr16 and several discrepancies in Chr17. Researchers - especially positional cloners - are strongly encouraged to use the tools provided (comparison plots, chromosome reports) to evaluate the accuracy of the assembly in specific regions of interest. Bulk downloads of the hg11 data should be available from this site in approximately one week. New annotation tracks will be posted as soon as they become available. Posted on 24 Apr. 2002 - Bulk Data Downloads of Mouse Assembly Feb. 2002 Available Bulk downloads of the February 2002 mouse genome assembly are now available from ftp://genome-archive.cse.ucsc.edu/goldenPath/mmFeb2002. You can also access the data from the archived downloads link. Posted on 19 Apr. 2002 - New Mouse Genome Assembly Released The February 2002 mouse genome assembly is now available in the browser and for BLAT searching. This assembly was produced at the Whitehead Institute using their Arachne software. We'd like to thank them and the Mouse Genome Sequencing Consortium for providing this assembly, which has specific conditions for use. Bulk downloads of the data should be available in approximately one week. Coordination with mouse genome data access at Ensembl and NCBI is in progress. We'd also like to acknowledge the UCSC team that produced this release: Jim Kent, Terry Furey, Matt Schwartz, Fan Hsu, Yontao Lu, Donna Karolchik, Chuck Sugnet, and Ryan Weber. Posted on 9 Apr. 2002 - Bulk Data Downloads of Mouse Assembly Nov. 2001 Available Bulk downloads of the November 2001 mouse genome assembly are now available from ftp://genome-archive.cse.ucsc.edu/goldenPath/mmNov2001. You can also access the data from the archived downloads link. Posted on 2 Apr. 2002 - Release of New Genome Browser Version and Mouse/Human Annotations An updated version of the UCSC Genome Browser (v.11) is now available. Along with the v.11 browser, we've released several new annotation tracks on the latest human and mouse assemblies. The new Human Dec. 2001 tracks include: Mouse Synteny, Ensembl, Genscan, CpG Islands, Mouse Blat, Fish Blat, Unigene/SAGE, NCI60 Microarray, GNF Affymetrix Microarray, Rosetta Microarray, and SNPs. An STS Markers track has been added to the Mouse Nov. 2001 browser. Posted on 14 Mar. 2002 - Mouse Draft Assembly Nov. 2001 Released in Genome Browser The November 2001 mouse genome assembly is now available for viewing in the browser and for BLAT searching. This assembly was produced at the Sanger Center using the Phusion software developed by Jim Mullikin and Zemin Ning, and was tied to the mouse fingerprint map by Tim Hubbard. We'd like to thank them and the Mouse Genome Sequencing Consortium for providing this assembly, which has specific conditions for use. Bulk downloads of the data will be available in approximately one week. Coordination with mouse genome data access at Ensembl and NCBI is in progress. We'd also like to acknowledge the UCSC team that produced this release: Jim Kent, Terry Furey, Matt Schwartz, Fan Hsu, Yontao Lu, and Donna Karolchik. Posted on 16 Feb. 2002 - Human Genome Assembly Build 28 Now Available A new assembly based on sequence submitted as of Dec. 22 in Genbank (Build 28) is now available in the browser and for BLAT search. This assembly was produced at NCBI rather than UCSC, primarily by Richa Agarwala, Greg Schuler, and Paul Kitts. The NCBI assembly has been steadily improving over the past year. Currently it shows slightly better local order and orientation compared to the UCSC assembly on the same sequence, but somewhat worse tracking of the chromosome level maps. The NCBI assembly has the advantage that it can be generated significantly faster than the UCSC assembly. With the human genome sequencing now in the end game - over two thirds of the human clones are now finished - we feel it more productive to focus worldwide annotation efforts on a single assembly rather than continue producing competing assemblies. We're working with NCBI to improve their map tracking. Posted on 4 Feb. 2002 - Chromosome Reports Released Chromosome Reports detailing correspondence with STS map, overlap, and BAC end sequence information are available under the "Technical Information About the Assembled Sequence" section below. This also gives information about the clone map on which the assembled sequence is based. Posted on 18 Dec. 2001 - New Genome Browser Enhancements There are some major enhancements to the browser. The complete user interface settings including track controls, labels, and position are now saved from session to session. You can configure the browser once to your liking and it will stay that way. This feature will only work if cookies are enabled in your browser. If you want to restore the default settings use the reset all button under the main graphic. Also under the main graphic are new controls that move just the start or just the end of the genome window. These are useful for getting exactly the right view without having to do arithmetic on the position. These controls by default will move two guideline units at a time, but you can specify other increments. There's a new page associated with each track. This page is accessible by clicking on the mini-buttons to the left of the track in the main graphic, or by clicking on the new hyperlink associated with the track in the track controls section under the graphic. These pages contain a description of the track and in many cases new controls. The mRNA and EST associated controls let you color or filter the display according to tissue, author, organism, and so forth. As with any new enhancement there are likely to be a few new bugs too. Many of these have been spotted and fixed already. Please let us know if you find a problem that persists more than a day or two. It's always helpful to include the freeze and genomic position with a problem report. Posted on 30 Nov. 2001 - Link Added to Jackson Lab's MGI Mouse Orthologs There is now a link from the known genes details page to the Jackson Lab's MGI Mouse Ortholog when the ortholog is known. Thanks to Carol Bult for her help setting up this link. Posted on 29 Nov. 2001 - Duplications Track Released for August Browser A duplications track is now available in the August browser. This track shows duplicate blocks of sequence larger than 1000 bases. The track is hidden by default. To open it look for 'Duplications' in the third row of track controls under the main graphic window, and change the setting to 'dense'. Thanks to Evan Eichler and Jeff Bailey for this track. Posted on 28 Nov. 2001 - Sanger Curated Gene Annotations Now Available on Chromosome 20 Sanger curated gene annotations are now available on chromosome 20. Thanks to Jennifer Ashurst, James Gilbert, and all the annotators at the Sanger Institute. Posted on 27 Nov. 2001 - Haplotype Blocks Annotation Released for Chromosome 21 A new track has been added to the August freeze browser showing haplotype blocks derived from common SNPs on Chromosome 21 by Perlegen, as described in "Common High-Resolution Haplotypes." Patil, N. et. al. Science 294:1719-1723 (2001). Posted on 19 Nov. 2001 - SNP and Mouse Blat Tracks Available The SNP and Mouse Blat tracks are now available for August. The Mouse Blat track uses a partial assembly of the public whole genome shotgun data courtesy of Whitehead's Arachne program. Posted on 8 Nov. 2001 - Interface of Track Details Pages Updated The detail web pages for each of the tracks have been updated to reflect the overall look and design of this site. You will now see the familiar blue navigation bar with links to the Browser, BLAT, Downloads, and the FAQ page from each of the track detail pages. Posted on 8 Nov. 2001 - STS Markers Track Updated on Apr. and Aug. Browsers The STS Markers track has been updated on the April and August browsers to now include much more information on the detail page including links to UniSTS and details on the alignments of the markers to the draft sequence. In addition, all known aliases of the markers can be entered in the "position" window, and the corresponding merker will be found and displayed if its location has been determined. Posted on 8 Nov. 2001 - FISH Clones Track Added to Apr. and Aug. Browsers A new FISH Clones track has been added to the April and August browsers. Previously, this information has been included in the STS Markers track. Now, this has been broken out into a separate track with additional information provided on the detail page not previously shown. Posted on 6 Nov. 2001 - Fgenesh++ Gene Predictions and Cross-Species mRNA Tracks Available The fgenesh++ gene prediction and the cross-species mRNA tracks are now available in the August browser. Posted on 31 Oct. 2001 - DNA Button Functionality Upgraded The 'DNA' button at the top of the browser has been significantly upgraded. By default it now returns DNA that has repeating elements in lower case and other DNA in upper case. There is also an option to color the DNA output with various tracks. You can have the case and font features such as underline, bold, and italic follow tracks too. Posted on 29 Oct. 2001 - TIGR Gene Index Track Added to April Browser There is now a TIGR Gene Index track in the April 2001 freeze browser. The TIGR Gene Index is based on alignments of assembled ESTs from a number of species. Be sure to click into the track and follow the outside links to the TIGR site, which contains a wealth of information on the genes. Posted on 29 Oct. 2001 - Acembly Track Updated on August Browser The Acembly track on the August 2001 freeze has been updated to include predictions based on human ESTs and Genbank mRNAs as well as RefSeq human mRNAs. Protein predictions are now also available in the details page for this track. The outside link for this track is also very informative. Posted on 27 Oct. 2001 - Share Your Custom Annotation Tracks! You can now share your custom tracks with the community. The easiest way to do this is to construct a link from your own web pages to the browser. Here is an example of a URL for such a link:
       http://genome.ucsc.edu/cgi-bin/hgTracks?
            position=chr22:1-20000&db=hg8&
            hgt.customText=http://genome.ucsc.edu/test.bed
The position variable tells the browser which part of the genome to display. The db variable refers to the freeze number. 'hg8' corresponds to the August 2001 freeze. The customText variable should refer to a URL containing plain text in one of the formats described in http://genome.ucsc.edu/goldenPath/help/customTrack.html. Note that generally we only keep the last three versions of the genome online (hg6, hg7, and hg8). You'll have to update your link and track about every 4 months as a result. Please send in the URLs of tracks you'd like to share to genome@soe.ucsc.edu, along with a brief description of the track and the genome version it is tied to. We'll create an index page of these here. You can also access an external custom track by including the URL of the track data (on a separate line starting with http://) in the custom track box at the bottom of the browser gateway. Posted on 15 Oct. 2001 - Weekly Updates of Tab-delimited Data Files Fresh tab-delimited files from the browser database are now available. They will now be updated automatically every Sunday evening. The table browser queries the database directly, so it is always up to the minute. Posted on 12 Oct. 2001 - New Gene Prediction Tracks for Apr. and Aug. Browsers Several new sets of gene predictions came in this week. We now have fgenesh++ predictions for the April freeze, and Genscan and Acembly predictions for the August freeze. Posted on 11 Oct. 2001 - Table Browser Upgraded Why struggle with massive genomic file downloads when the UCSC Table Browser lets you select exactly the track data desired via a convenient web interface? Major new improvements by Krish Roskin have empowered and simplified this feature available now for the three most recent assemblies. Posted on 8 Oct. 2001 - Oct. 2000 Assembly Moved to Archives The October 2000 assembly has been moved to the Archives to make room for the August assembly. Posted on 5 Oct. 2001 - Revised Aug. 2001 Assembly Released A revised August 2001 freeze assembly is now up. The problems with flipped contigs of finished clones and high levels of sequence duplication are fixed. You can now download this assembly in bulk as well as browse it. Chromosome by chromosome and annotation database files will be following over the next day or two. Posted on 2 Oct. 2001 - Convert Coordinates Between Different Draft Assemblies You can now convert coordinates between different versions of the draft using a new program, hgCoordConv, by Chuck Sugnet. hgCoordConv attempts to cut out sequences of the original draft and align them to the new draft. When aligning the sequences to the new draft hgCoordConv makes sure that the sequences are in the same order, orientation, and have the correct distances between them. Chuck has also implemented a SAGE/Unigene track in the browser. This track displays data from the SAGEMap project at NCBI . UniGene cluster sequences are displayed in the browser and colored according to their average SAGE counts over a series of experiments. Selecting one of the UniGene representative sequences displays the SAGE results for UniGene sequences. Posted on 21 Sep. 2001 - Clone Order Problems Found in Preliminary Aug. 2001 Assembly Some systematic problems were found in the clone order on the preliminary August 2001 freeze assembly. The sequencing center at Washington University, EBI's Ensembl group, and our group here at UCSC are currently working together to revise the merged BAC clone maps and the assembly process to fix these problems. We hope to update the August browser with a revised assembly soon. Then, after further testing via the browser, we will release the assembled August freeze genome sequence itself. Posted on 11 Sep. 2001 - Preliminary Aug. 2001 Assembly Now Available in Genome Browser A preliminary assembly of the August 2001 freeze is now available in the genome browser. Due to significant progress by the mapping and finishing groups of the international public consortium, this assembly is a major improvement over the April 2001 freeze assembly. Imre Vastrik, Ewan Birney and colleagues at Ensembl have computed a merge of BAC clone maps provided by the individual sequencing centers with fingerprint-based maps prepared at Washington University. These merged maps were used for the first time in this August assembly. The August assembly has successfully passed our internal quality control tests. We will release the sequence and annotations in bulk downloadable form in a week or so, after the external testers have had a chance to further verify it. Meanwhile if you notice any systematic problems please let us know at genome@soe.ucsc.edu. Though the state of the working draft has improved considerably, remember that where you see solid marks in the 'gap' track, the relative order and orientation of flanking contigs is still uncertain. In some cases of complex repeat structure it is also possible that the assembly may be incorrect even in the absence of gaps. Also, sometimes ambiguities in the data cause a BAC clone to be split, with parts of it placed at opposite ends of a run of other clones. Localized errors of this type should be corrected by additional finishing efforts at the individual sequencing centers and should not be reported to UCSC. However, please report any large-scale or systematic problems you detect with this assembly that could have been caused by our data processing. The tracks available on the August 2001 browser are quite limited at the moment. More tracks will show up over time. Posted on 11 Sep. 2001 - April 2001 Assembly is New Default in Genome Browser The April 2001 assembly is now the default for the browser. The SNP and Ensembl gene tracks have come in for this version. There is also a new track depicting non-human vertebrate mRNA alignments. The Sept. 2000 and July 2000 versions of the genome are now only available on our archive site. Please see the link in the blue box to the left for more details. The August 6 freeze is progressing through the pipeline. We've recently received an updated accession map from Wash U. Ensembl will shortly be integrating this with chromosome specific maps from the sequencing centers. We are still on track for an early September next release. Posted on 28 Aug. 2001 - Custom Annotation Track Functionality Added Meanwhile we've been continuing work on the genome browser. It's now possible to upload your own annotations to be displayed alongside the built-in tracks. Please scroll to the bottom of the browser gateway pages for further information. The browser has also been sped up, particularly on the larger chromosomes by using a 'binning' technique suggested by Lincoln Stein and Richard Durbin. Posted on 23 Aug. 2001 - New Annotation Tracks on April 2001 Browser Tracks continue to be added to the April 2001 browser. Our old friend the Exofish track is back. The blat mouse homology track is now up as well, computed at somewhat more sensitive settings than it was in the December 2000 browser. We've recently received some significant funding from NHGRI to maintain and extend this site. This has allowed us among other things to hire an artist, Jenny Draper, who is responsible for the new look. |
Freeze-Specific News Archives
| 1 Apr. 2001 Freeze 13 Jul. 2001: fixed bug where some UTRs were mis-annotated in the known genes on the minus strand. 12 Dec. 2000 Freeze 13 Jul. 2001: fixed bug where some UTRs were mis-annotated in the known genes on the minus strand. 5 Apr. 2001: chromosome level files (but not contig level files) updated to fix bug where some of the centromeres were misplaced 1 Apr. 2001: chromosome Y updated to fix a bug that put a large gap between each clone. This bug was limited to the Y chromosome. 7 Oct. 2000 Freeze 7 Apr. 2001: Affymetrix gene predictions updated and available for bulk download. 9 Jan. 2001: all files were updated after a bug that had caused some finished clones to be flipped in the assembly was caught and fixed. Our apologies for any inconvenience this has caused. 10 Nov. 2000: the sequence (.fa) files for two contigs: X/ctg18523/ctg18523.fa and 7/ctg15082/ctg15082.fa were updated. These files had null (zero valued) characters that have been replaced with N characters. These characters were a result of a mismatch between clone sizes in the map and in finished NT contigs. The sequence for chromosomes X and 7, which contain these contigs, has also been updated. 5 Sep. 2000 Freeze 11 Oct. 2000: chr21.agp and chr22.fa were updated. chr21.agp was a version which went with the UCSC draft assembly rather than the Sanger/NCBI final assembly of this chromosome. chr21.agp and chr21.fa are now in sync. chr22.fa and chr22.agp were also previously out of sync. chr22.fa was obtained from Sanger while chr22.agp had been obtained by NCBI. With this update they are consistent, both NCBI versions. Apologies for any rework this causes you. 9 Oct. 2000: chr21_random.* and chr22_random.* were removed from the zip-files in the September 5th freeze. These files were relics that should not have been included in the first place. The files chr9_random.agp, chr10_random.agp, chr11_random.agp, chr12_random.agp, chr13_random.agp and chr14_random.agp were updated. There was a bug where the initial field of the initial lines in these files was "(null)" rather than "chrN_random" as it should have been. 17 Jul. 2000 Freeze 22 Sep. 2000: The zip-files chromFa.zip and chromAgp.zip under the July 17th full data set were updated to fix some duplications of clone contigs that occurred in the chrN_random.agp and chrN_random.fa files contained within these zip-files. These "_random" files are files that contain clone contigs that were mapped to a particular chromosome, but could not be placed at a specific position within that chromosome. They correspond to the "RANDOM" sections of the WashU map. None of the regular chrN.agp or chrN.fa files were affected by this update, nor was any of the information in the contigAgp.zip or contigFa.zip files changed. For convenience, we include two new files, chromRandAgp.zip and chromRandFa.zip, for users who would like to download only the data that has changed. These zips consist of the updated chrN_random.agp and chrN_random.fa files, respectively. 4 Sep. 2000: The files chromFa.zip and contigFa.zip under the July 17th full data set and the files under July 17th data by individual clone contig were updated to fix some incorrect (null(0)) characters that needed to be replaced by 'n' characters in some Fasta files. The following contig Fasta files on chromosomes 1,8,11,12,16, 17 and 19 were affected:
    1/ctg14250/ctg14250.fa
    8/ctg17325/ctg17325.fa
    8/ctg16307/ctg16307.fa
    8/ctg25150/ctg25150.fa
    8/ctg15216/ctg15216.fa
    11/ctg15548/ctg15548.fa
    12/ctg15285/ctg15285.fa
    16/ctg16864/ctg16864.fa
    16/ctg28077/ctg28077.fa
    16/ctg13970/ctg13970.fa
    16/ctg25401/ctg25401.fa
    16/ctg13336/ctg13336.fa
    16/ctg14937/ctg14937.fa
    16/ctg16860/ctg16860.fa
    16/ctg17794/ctg17794.fa
    17/ctg14047/ctg14047.fa
    19/ctg16564/ctg16564.fa
We apologize for any inconvenience this may have caused. |