UCSC Genome Browser Acknowledgments
| The data and software displayed on this site are the result of a large collaborative effort among many individuals at UCSC and at research institutions around the world. We'd like to acknowledge the scientists and engineers who have contributed to the UCSC Genome Browser and its data, and the organizations who have made this project possible through their generous funding. Human Genome Cat Genome Chicken Genome Chimpanzee Genome Cow Genome Dog Genome Elephant Genome Fugu Genome Gibbon Genome Gorilla Genome Guinea Pig Genome Horse Genome Lamprey Genome Lancelet Genome Lizard Genome Marmoset Genome Medaka Genome Microbat Genome Mouse Genome Opossum Genome Orangutan Genome Panda Genome Pig Genome Platypus Genome Rabbit Genome Rat Genome Rhesus Genome Sheep Genome Stickleback Genome Tetraodon Genome Turkey Genome X. tropicalis Genome Zebra finch Genome Zebrafish Genome C. intestinalis Genome S. purpuratus Genome A. gambiae Genome A. mellifera Genome D. ananassae Genome D. erecta Genome D. grimshawi Genome D. melanogaster Genome D. mojavensis Genome D. persimilis Genome D. pseudoobscura Genome D. sechellia Genome D. simulans Genome D. virilis Genome D. yakuba Genome C. brenneri Genome C. briggsae Genome C. elegans Genome C. japonica Genome C. remanei Genome P. pacificus Genome Yeast Genome California Sea Hare Genome Other scientists featured on this site Acknowledgements of early support Click here to view the contributions of the UCSC Genome Browser project team. |
Human Genome: Acknowledgements
The UCSC Human Genome Browser Project is conducted in collaboration with the International Human Genome Project. We have worked with many collaborators at other institutions to produce and annotate this reference sequence of the human genome, as described in our recent publications. The UCSC Human Genome Project is made possible by a grant from the National Human Genome Research Institute, directed by Francis Collins, and generous support from the Howard Hughes Medical Institute and the California Institutes for Science and Innovation. The UCSC Human Genome Browser is generated by the UCSC Genome Bioinformatics Group, and annotations are produced by UCSC and collaborators at other institutions. The UCSC staff responsible for producing the initial hg19 browser include Hiram Clawson, Brooke Rhead, Pauline Fujita, Ann Zweig, Katrina Learned, and Robert Kuhn. To view complete acknowledgements for a specific annotation, see the "Credits" section on the annotation track's description page in the Genome Browser. |
Human Genome: Data Sources
| Starting with the hg19 assembly, the human genome sequence is provided by the Genome Reference Consortium (GRC), 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. Prior to hg19, the human genome sequence data used in the browser were generated by laboratories belonging to the Human Genome Sequencing Consortium. Periodic freezes of this data were generated by NCBI, and EST, mRNA, BACend and other types of data used for the assembly and annotation were obtained from GenBank /EMBL /DDBJ. Clone maps were created by the individual sequencing centers. The original chromosome files were produced by the institutions and people listed in the table below.
Finished Chromosomes
Chr. # | Sequencing Centers | AGP File
1 | The Sanger Institute, Cambridge, UK. University of Washington Genome Center, Seattle, WA, USA | Jane Rogers
2 | Washington University School of Medicine Genome Sequencing Center, St Louis, MO, USA | Rick Wilson
3 | Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA Beijing Human Genome Center, Beijing, China University of Washington Genome Center, Seattle, WA, USA | Steve Scherer
4 | Washington University School of Medicine Genome Sequencing Center, St Louis, MO, USA Stanford Human Genome Center, Palo Alto, CA, USA | Rick Wilson
5 | Joint Genome Institute, U.S. Department of Energy, Walnut Creek, CA, USA Stanford Human Genome Center (Myers), Palo Alto, CA, USA | Jeremy Schmutz
6 | The Sanger Institute, Cambridge, UK. | Jane Rogers
7 | Washington University School of Medicine Genome Sequencing Center, St Louis, USA University of Washington Genome Center, Seattle, WA, USA | Rick Wilson
8 | The Broad Institute, USA Keio University, Tokyo, Japan Institute of Molecular Biology (IMB), Jena, Germany | Chad Nusbaum
9 | The Sanger Institute, Cambridge, UK. Gesellschaft für Biotechnologische Forschung (GBF), Braunschweig, Germany | Jane Rogers
10 | The Sanger Institute, Cambridge, UK. Genome Therapeutics Corporation (GTC), Waltham, MA, USA | Jane Rogers
11 | RIKEN Human Genome Research Group, Saitama, Japan The Broad Institute, USA | Todd Taylor
12 | Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA | Steve Scherer
13 | The Sanger Institute, Cambridge, UK. | Jane Rogers
14 | Genoscope National Sequencing Centre, Evry, France Institute for Systems Biology (ISB), Seattle, WA Washington University School of Medicine Genome Sequencing Center, St Louis, USA RIKEN Human Genome Research Group, Saitama, Japan | Jean Weissenbach
15 | The Broad Institute, USA Institute of Molecular Biology (IMB), Jena, Germany Institute for Systems Biology (ISB), Seattle, WA | Chad Nusbaum
16 | Joint Genome Institute (JGI), U.S. Department of Energy, Walnut Creek, CA, USA Stanford Human Genome Center, Palo Alto, CA, USA The Institute for Genomic Research (TIGR), Rockville, MD, USA The Sanger Institute, Cambridge, UK. | Jeremy Schmutz
17 | The Broad Institute , USA | Chad Nusbaum
18 | The Broad Institute, USA RIKEN Human Genome Research Group, Saitama, Japan | Chad Nusbaum
19 | Joint Genome Institute (JGI), U.S. Department of Energy, Walnut Creek, CA, USA Stanford Human Genome Center, Palo Alto, CA, USA | Jeremy Schmutz
20 | The Sanger Institute, Cambridge, UK. | James Gilbert
21 | RIKEN Human Genome Research Group, Japan Max Planck Institute for Molecular Genetics, Berlin, Germany Gesellschaft für Biotechnologische Forschung (GBF), Braunschweig, Germany Keio University School of Medicine, Tokyo, Japan Chromosome 21 Consortium | Todd Taylor
22 | The Sanger Institute, Cambridge, UK. The University of Oklahoma, USA. Keio University School of Medicine, Tokyo, Japan | Jane Rogers
X | The Sanger Institute, Cambridge, UK. Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA Institute of Molecular Biology (IMB), Jena, Germany Washington University School of Medicine Genome Sequencing Center, St Louis, USA Max Planck Institute for Molecular Genetics, Berlin, Germany | Jane Rogers
Y | Washington University School of Medicine Genome Sequencing Center, St Louis, USA | Rick Wilson
Chimpanzee Genome
| The UCSC Chimpanzee Genome Browsers display draft assembly data produced by the Chimpanzee Genome Sequencing Consortium: Oct. 2010 panTro3 browser: v2.1.3 chromosome-based 6X draft assembly (Oct. 2010) Mar. 2006 panTro2 browser: v2.1 chromosome-based 6X draft assembly (Oct. 2005) Nov. 2003 panTro1 browser: v1.1 Arachne draft assembly The Chimp Genome Browsers have the the following acknowledgements: Funding: National Human Genome Research Institute (NHGRI) Sequencing/Assembly (panTro2): Whole genome shotgun (WGS) sequence data assembly and organization: Washington University School of Medicine Genome Sequencing Center (GSC), St. Louis, MO, USA Underlying WGS data: Washington University School of Medicine GSC and the Broad Institute 5-Mb region of chromosome 7 at chr7:84674857-89461887): finished by Washington University GSC Chromosome Y sequence: finished by Washington University GSC with detailed mapping and extensive collaboration with David Page's group at the Whitehead Institute. For more information, see: Hughes et al. Conservation of Y-linked genes during human evolution revealed by comparative sequencing in chimpanzee. Nature. 2005 437(7055):100-3. "The DNA Sequence of Chimpanzee Chromosome Y", unpublished. Chromosome 21 sequence: Todd Taylor and the RIKEN Genomic Sciences Center. See Watanabe et al. DNA sequence and comparative analysis of chimpanzee chromosome 22. Nature. 2004 May27;429(6990):382-8. Sequencing/Assembly (panTro1): Sequence assembled by teams led by Eric Lander, Ph.D. at the Broad Institute and Richard K. Wilson, Ph.D. at the Washington University School of Medicine GSC, St. Louis, MO, USA Alignments: LaDeana Hillier, Washington University School of Medicine GSC and the Broad Institute Annotations: Washington University School of Medicine GSC, St. Louis, MO, USA Research Group on Biomedical Informatics of IMIM/UPF (GRIB), Barcelona, Spain Riken Genomic Sciences Center, Yokohama City, Japan UCSC Genome Bioinformatics Group, Santa Cruz, CA, USA UCSC Chimp Genome Browser (panTro3): Hiram Clawson, Greg Roe, and Donna Karolchik UCSC Chimp Genome Browser (panTro2): Kate Rosenbloom, Brian Raney, Hiram Clawson, Ann Zweig, Archana Thakkapallayil, and Donna Karolchik UCSC Chimp Genome Browser (panTro1): Kate Rosenbloom, Jim Kent, Hiram Clawson, Heather Trumbower, Robert Kuhn, and Donna Karolchik The chimpanzee sequence is made freely available before scientific publication from the Chimpanzee Genome Sequencing Consortium with the following understanding: The data may be freely downloaded, used in analyses, and repackaged in databases. Users are free to use the data in scientific papers analyzing particular genes and regions if the providers of this data (the Chimpanzee Genome Sequencing Consortium) are properly acknowledged. The centers producing the data reserve the right to publish the initial large-scale analyses of the data set, including large-scale identification of regions of evolutionary conservation and large-scale genomic assembly. Large-scale refers to regions with size on the order of a chromosome (that is, 30 Mb or more). Any redistribution of the data should carry this notice. |
Rhesus Genome
| The sequencing and assembly of the Macaca mulatta genome is a project of the Macaque Genome Sequencing Consortium led by the Baylor College of Medicine Human Genome Sequencing Center, in collaboration with the J. Craig Venter Institute Joint Technology Center, and the Genome Sequencing Center at Washington University School of Medicine, St. Louis. Jan. 2006 rheMac2 Genome Browser: Jan. 2006 draft assembly of the rhesus monkey, version Mmul_051212 from Baylor College of Medicine Human Genome Sequencing Center (BCM HGSC) Jan. 2005 rheMac1 Genome Browser: Jan. 2005 draft assembly of the rhesus monkey, version Mmul_0.1. This assembly is provided with the following acknowledgements: Funding: National Human Genome Research Institute (NHGRI), USA Sequencing/Assembly: BCM HGSC, Houston, TX, USA in collaboration with: J. Craig Venter Science Foundation Joint Technology Center, Rockville, MD, USA Genome Sequencing Center at Washington University School of Medicine, St. Louis, MO, USA BAC resources: Children's Hospital Oakland Research Institue (CHORI), Oakland, CA, USA BAC-based fingerprint map: Genome Sciences Centre, Vancouver, B.C. UCSC Rhesus Genome Browser (rheMac2) and Initial Annotations: UCSC Genome Bioinformatics Group, Santa Cruz, CA, USA - Robert Baertsch, Kayla Smith, Ann Zweig, Robert Kuhn, and Donna Karolchik. UCSC Rhesus Genome Browser (rheMac1) and Initial Annotations: UCSC Genome Bioinformatics Group, Santa Cruz, CA, USA - Robert Baertsch, Galt Barber, and Donna Karolchik. For more information on the rhesus genome project, see the BCM HGSC Rhesus Monkey Genome Project web page. These data are made available before scientific publication with the following understanding: The data may be freely downloaded, used in analyses, and repackaged in databases. Users are free to use the data in scientific papers analyzing particular genes and regions if the providers of this data (Baylor College of Medicine Human Genome Sequencing Center and the Rhesus Macaque Genome Sequencing Consortium) are properly acknowledged. Please cite the BCM-HGSC web site or publications from BCM-HGSC referring to the genome sequence. The BCM-HGSC and RMGSC plan to publish the assembly and genomic annotation of the dataset, including large-scale identification of regions of evolutionary conservation. This is in accordance with, and with the understandings in the Fort Lauderdale meeting discussing Community Resource Projects and the resulting NHGRI policy statement. Any redistribution of the data should carry this notice. |
Cat Genome
| The UCSC felCat4 Genome Browser displays data from the Dec. 2008 catChrV17e draft assembly, based on sequence reads from six domestic cats and one wild cat. The browser was produced with the following acknowledgements: Sequencing/Assembly: NHGRI Genome Technology Branch and NIH Intramural Sequencing Center, Bethesda, MD, USA Agencourt Bioscience Corporation, Danvers, MA, USA NCI Laboratory of Genomic Diversity, Frederick, MD, USA Hill's Pet Nutrition, Inc., Topeka, KS, USA UCSC Cat Genome Browser/Initial Annotations (felCat4): UCSC Genome Bioinformatics Group, Santa Cruz, CA, USA - Chin Li, Hiram Clawson, Antonio Coelho, Mary Goldman, and Donna Karolchik The UCSC felCat3 Genome Browser displays data from the March 2006 v3 draft assembly of the domestic cat (Felis catus). This assembly was provided with the following acknowledgements: Funding: The National Human Genome Research Institute Project Leadership: The Broad Institute, Cambridge, MA, USA Sequencing/Assembly: The Broad Institute, Cambridge, MA, USA - Team led by by Kerstin Lindblad-Toh, Ph.D. Plasmid and fosmid libraries: The Broad Institute, Cambridge, MA, USA BAC end sequencing: Agencourt Bioscience, Beverly, MA, USA UCSC Cat Genome Browser/Initial Annotations (felCat3): UCSC Genome Bioinformatics Group, Santa Cruz, CA, USA - Heather Trumbower, Angie Hinrichs, Mark Diekhans, Brooke Rhead, and Archana Thakkapallayil The cat sequence is made freely available before scientific publication with the following understanding: The data may be freely downloaded, used in analyses, and repackaged in databases. Users are free to use the data in scientific papers analyzing particular genes and regions if the providers of these data are properly acknowledged. The centers producing the data reserve the right to publish the initial large-scale analyses of the data set, including large-scale identification of regions of evolutionary conservation and large-scale genomic assembly. Large-scale refers to regions with size on the order of a chromosome (that is, 30 Mb or more). Any redistribution of the data should carry this notice. |
Dog Genome
| The UCSC Dog Genome Browser displays data from the July 2004 v1.0 (canFam1) and May 2005 v2.0 (canFam2) draft assemblies of the domestic dog (Canis familiaris). These assemblies are provided with the following acknowledgements: Funding: The National Human Genome Research Institute Project Leadership: The Broad Institute, Cambridge, MA, USA Sequencing/Assembly: The Broad Institute, Cambridge, MA, USA - Team led by by Kerstin Lindblad-Toh, Ph.D. Plasmid and fosmid libraries: The Broad Institute, Cambridge, MA, USA BAC libraries: Children's Hospital Oakland Research Institute (CHORI), Oakland, CA, USA BAC end sequencing: Agencourt Bioscience, Beverly, MA, USA RH map: Centre National de la Recherche Scientifique (CNRS), France FISH mapping: North Carolina State University (NCSU), Raleigh, NC, USA Dog Selection: Fred Hutchinson Cancer Research Center (FHCRC), Seattle, WA, USA UCSC Dog Genome Browser/Initial Annotations (canFam2): UCSC Genome Bioinformatics Group, Santa Cruz, CA, USA - Angie Hinrichs, Jennifer Jackson, and Donna Karolchik UCSC Dog Genome Browser/Initial Annotations (canFam1): UCSC Genome Bioinformatics Group, Santa Cruz, CA, USA - Angie Hinrichs, Robert Kuhn and Donna Karolchik The dog genome sequence is made freely available by the Dog Genome Sequencing Project. Please cite the following publication when using these data: Lindblad-Toh K, et al. Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature. 2005 Dec 8;438:803-19. |
Cow Genome
| The UCSC Cow Genome Browser displays two different assemblies of the bovine genome: one provided by the University of Maryland Center for Bioinformatics and Computational Biology (UMD CBCB) and one from the Baylor College of Medicine Human Genome Sequencing Center (BCM HGSC). The assemblies available in the browser include: Nov. 2009 (bosTau6) assembly - UMD CBCB version UMD_3.1 Oct. 2007 (bosTau4) assembly - BCM HGSC version Btau_4.0 Aug. 2006 (bosTau3) assembly - BCM HGSC version Btau_3.1 Mar. 2005 (bosTau2) assembly - BCM HGSC version Btau_2.0 Sep. 2004 (bosTau1) assembly - BCM HGSC version Btau_1.0 The UMD CBCB genome assembly is provided with the following acknowledgements: Genome sequence: NCBI Trace Archive Genome assembly: University of Maryland Center for Bioinformatics and Computational Biology, College Park, MD, USA UCSC Cow Genome Browser/Initial Annotations (bosTau6): UCSC Genome Bioinformatics Group, Santa Cruz, CA, USA - Hiram Clawson, Chin Li, Brooke Rhead, Greg Roe, Steve Heitner, and Donna Karolchik The BCM HGSC genome assemblies are provided with the following acknowledgements: Funding - For a list of the many agencies that funded the cow sequencing project, see the BCM HGSC Bovine Genome Project page. BAC library DNA: Dr. Michael MacNeil's laboratory at the USDA Agricultural Research Service, Miles City, MT, USA Whole genome shotgun sequence DNA: Dr. Timothy Smith's laboratory at the U.S. Meat Animal Research Center, Clay Center, NE, USA BAC-based fingerprint map: Genome Sciences Centre, Vancouver, B.C. UCSC Cow Genome Browser/Initial Annotations (bosTau4): UCSC Genome Bioinformatics Group, Santa Cruz, CA, USA - Hiram Clawson, Brian Raney, and Ann Zweig. UCSC Cow Genome Browser/Initial Annotations (bosTau3): UCSC Genome Bioinformatics Group, Santa Cruz, CA, USA - Heather Trumbower, Angie Hinrichs, Kayla Smith and Donna Karolchik. UCSC Cow Genome Browser/Initial Annotations (bosTau2): UCSC Genome Bioinformatics Group, Santa Cruz, CA, USA - Galt Barber, Brian Raney, Mark Diekhans, Jennifer Jackson, and Donna Karolchik. UCSC Cow Genome Browser/Initial Annotations (bosTau1): UCSC Genome Bioinformatics Group, Santa Cruz, CA, USA - Heather Trumbower, Jim Kent, Hiram Clawson, Angie Hinrichs, Brian Raney, Mark Diekhans, Robert Kuhn, Ali Sultan-Qurraie and Donna Karolchik. Please acknowledge the appropriate institution when using these data sets. Citation information may be obtained from the UMD CBCB Bos taurus assembly page and the BCM HGSC Bovine Genome Project page. |
Mouse Genome
| The UCSC Mouse Genome Project is conducted in collaboration with the Mouse Sequencing Consortium and the Mouse Genome Sequencing Consortium. The mouse draft assembly displayed in the Genome Browser is assembled at NCBI. The initial 3X coverage of the mouse genome was produced by the Mouse Sequencing Consortium, with the following acknowledgements: Project Oversight: Arthur Holden and Francis Collins Funding: GlaxoSmithKline Merck Genome Research Institute Affymetrix, Inc. The Wellcome Trust The National Institutes of Health Sequencing: The Broad Institute Washington University St. Louis Genome Sequencing Center The Wellcome Trust Sanger Institute Later releases of the assembly and map have been produced by the Mouse Genome Sequencing Consortium, with these acknowledgements: Funding: National Institutes of Health The Wellcome Trust GlaxoSmithKline The Merck Genome Research Institute Affymetrix Sequencing: The Broad Institute's Arachne Group The Wellcome Trust Sanger Institute Washington University in St. Louis Genome Sequencing Center Baylor College of Medicine Human Genome Sequencing Center Wolfson Institute for Biomedical Research University of Oklahoma, Advanced Center for Genome Technology UK MRC Mouse Genome Centre and Mammalian Genetics Unit National Institutes of Health Intramural Sequencing Center Harvard Partners Genome Center Cold Springs Harbor Laboratory Physical Map: Mouse BAC libraries - Children's Hospital Oakland Research Institute (CHORI) BAC fingerprint map - Genome Sciences Centre BAC end sequences - The Institute of Genome Research (TIGR) TPF production - Tina Graves, April Cook, Christine Burton, Darren Graham, Shannon Dugan, Donna Muzny Assembly: Deanna Church, Richa Agarwala, Josh Cherry, Mike DiCuccio, Hsiu-Chuan Chen, Paul Kitts, Victor Sapojnikov cDNA Sequencing: Riken Institute The Mammalian Gene Collection UCSC Mouse Genome Browser (mm9): Hiram Clawson, Archana Thakkapallayil, Robert Kuhn and Donna Karolchik UCSC Mouse Genome Browser (mm8): Hiram Clawson, Fan Hsu, Kayla Smith, Ann Zweig, Robert Kuhn, Brooke Rhead, Archana Thakkapallayil, and Donna Karolchik UCSC Mouse Genome Browser (mm7): Hiram Clawson, Fan Hsu, Ann Zweig, Kayla Smith, Robert Kuhn and Donna Karolchik UCSC Mouse Genome Browser (mm6): Hiram Clawson, Fan Hsu, Jennifer Jackson, Robert Kuhn, Ali Sultan-Qurraie, Heather Trumbower and Donna Karolchik Annotations: UCSC Genome Bioinformatics Group The Jackson Laboratory NCBI Ensembl Pennsylvania State University University of California Berkeley/LBNL Mouse genome sequence data are released weekly into a public repository maintained by EBI and NCBI. References to these data should cite the following publication: Mouse Genome Sequencing Consortium. Initial sequencing and comparative analysis of the mouse genome. Nature, 420, 520-562 (2002). |
Rat Genome
| The UCSC Rat Genome Project is conducted in collaboration with the Rat Genome Sequencing Consortium. The Rat genome sequence was produced with the following acknowledgements: Project Coordination: Baylor College of Medicine Human Genome Sequencing Center, Richard Gibbs, director Funding: National Human Genome Research Institute (NIH) National Heart, Lung and Blood Institute (NIH) Sequencing: Baylor College of Medicine Human Genome Sequencing Center Celera Genomics Group of Applera Corporation Genome Therapeutics Corporation The University of Utah Assembly: Baylor College of Medicine Human Genome Sequencing Center ATLAS group - Rui Chen, James Durbin, Paul Havlak Fingerprint Mapping: The British Columbia Cancer Agency Genome Sciences Center - Marco Marra, Jackie Schein BAC End Sequencing: The Institute for Genomic Research - Shaying Zhao BAC Library Construction and Distribution: Children's Hospital Oakland Research Institute (CHORI) - Pieter deJong Rat Genome Database: Medical College of Wisconsin UCSC Rat Genome Browser (rn4) - Angie Hinrichs, Fan Hsu, Brooke Rhead, Archana Thakkapallayil, Kayla Smith, Ann Zweig, Robert Kuhn, and Donna Karolchik UCSC Rat Genome Browser (rn3) - Hiram Clawson, Heather Trumbower, Robert Kuhn, Yontao Lu, Terry Furey, Mark Diekhans, Robert Baertsch, Donna Karolchik, and Jim Kent The rat genome sequence is made freely available by the Rat Genome Project at the Baylor College of Medicine Human Genome Sequencing Center. Please cite the following publications when using these data: Havlak, P. et al. The Atlas genome assembly system. Genome Res. 14(4), 721-32 (2004). Rat Genome Sequencing Project Consortium. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature 428(6982), 493-521 (2004). See the Baylor data use limitations web page for restrictions on the use of these data. |
Opossum Genome
| The UCSC Opossum Genome Browser displays data from the draft assemblies of the opossum (Monodelphis domestica) produced by The Broad Institute. These assemblies are provided with the following acknowledgements: Sequencing/Assembly: The Broad Institute, Cambridge, MA, USA FISH Mapping: North Carolina State University (NCSU), Raleigh, NC, USA UCSC Opossum Genome Browser/Initial Annotations (monDom5): UCSC Genome Bioinformatics Group, Santa Cruz, CA, USA - Andy Pohl, Hiram Clawson, Brian Raney, Mark Diekhans, Brooke Rhead and Katrina Learned UCSC Opossum Genome Browser/Initial Annotations (monDom4): UCSC Genome Bioinformatics Group, Santa Cruz, CA, USA - Hiram Clawson, Archana Thakkapallayil, Ann Zweig, Kayla Smith and Donna Karolchik UCSC Opossum Genome Browser/Initial Annotations (monDom1): UCSC Genome Bioinformatics Group, Santa Cruz, CA, USA - Hiram Clawson, Galt Barber, Ali Sultan-Qurraie, Brian Raney and Donna Karolchik The opossum sequence is made freely available before scientific publication with the following understanding: The data may be freely downloaded, used in analyses, and repackaged in databases. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data (The Broad Institute) is properly acknowledged. The center producing the data reserves the right to publish the initial large-scale analyses of the data set, including large-scale identification of regions of evolutionary conservation and large-scale genomic assembly. Large-scale refers to regions with size on the order of a chromosome (that is, 30 Mb or more). Any redistribution of the data should carry this notice. |
Orangutan Genome
| The UCSC Orangutan Genome Browser displays data from the draft assemblies of the Sumatran orangutan (Pongo pygmaeus abelii), which are provided with the following acknowledgements: Sequencing: The Genome Sequencing Center at Washington University School of Medicine (WUSTL), St. Louis, MO, USA Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA Sequence Assembly and Chromosomal Sequence/AGP Construction: WUSTL DNA Source: Dr. Greely Stones - Gladys Porter Zoo, Brownsville, TX, USA BAC Library: Yuko Yoshonaga in Pieter de Jong's laboratory - Children's Hospital Oakland Research Institute, Oakland, CA, USA Fosmid Library: WUSTL Fingerprint Map: WUSTL Cytogenetic Mapping and Human/Orangutan Breakpoint Analyses: Mariano Rocchi - Department of Genetics and Microbiology, University of Bari, Bari, Italy Fosmid End Placement against the Human Genome (used for breakpoint/inversion analyses during AGP construction): Lin Chen, Evan Eichler - Department of Genome Sciences, University of Washington, Seattle, WA, USA Funding: National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH) UCSC Orangutan Genome Browser/Initial Annotations (ponAbe2): UCSC Genome Bioinformatics Group, Santa Cruz, CA, USA - Hiram Clawson, Kayla Smith, Robert Kuhn, Ann Zweig and Donna Karolchik The orangutan sequence is made freely available before scientific publication with the following understanding: The data may be freely downloaded, used in analyses, and repackaged in databases. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data (Genome Sequencing Center at WUSTL) is properly acknowledged. The centers producing the data reserve the right to publish the initial large-scale analyses of the data set, including large-scale identification of regions of evolutionary conservation and large-scale genomic assembly. Large-scale refers to regions with size on the order of a chromosome. This is in accordance with, and with the understandings in the Fort Lauderdale meeting discussing Community Resource Projects and the resulting NHGRI policy statement. Any redistribution of the data should carry this notice. |
Gibbon Genome
| The UCSC Gibbon Genome Browser displays data from the draft assemblies of the northern white-cheeked gibbon (Nomascus leucogenys) provided with the following acknowledgements: Sequencing and Assembly: The Genome Institute at Washington University School of Medicine (WUSTL), St. Louis, MO, USA Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA Funding: National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH) UCSC Gibbon Genome Browser/Initial Annotations (nomLeu1): UCSC Genome Bioinformatics Group, Santa Cruz, CA, USA - Chin Li, Brooke Rhead, Steve Heitner, Lauren Scott and Donna Karolchik The gibbon sequence is made freely available before scientific publication. Please review the Genome Institute at WUSTL data use policy and the Baylor College of Medicine conditions for use guidelines before using these data. |
Gorilla Genome
| The UCSC Gorilla Genome Browser displays the draft assembly of the gorilla genome (Gorilla gorilla gorilla) provided with the following acknowledgements: Sequencing: The Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK Assembly: The Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK The European Bioinformatics Institute (EBI), Hinxton, Cambridge, UK UCSC Gorilla Genome Browser/Initial Annotations (gorGor3): UCSC Genome Bioinformatics Group, Santa Cruz, CA, USA - Hiram Clawson, Mark Diekhans, Brian Raney, Brooke Rhead, Steve Heitner, Lauren Scott and Donna Karolchik The gorilla sequence is made freely available to the public by the Wellcome Trust Sanger Institute. Please review their data-sharing policy before using these data. |
Guinea Pig Genome
| The UCSC Guinea Pig Genome Browser displays data from the Feb. 2008 CavPor3 draft assembly of the guinea pig (Cavia porcellus) from the Broad Institute. This assembly is provided with the following acknowledgements: Funding: The National Human Genome Research Institute Sequencing/Assembly: The Broad Institute, Cambridge, MA, USA UCSC Guinea Pig Genome Browser/Initial Annotations (cavPor3): UCSC Genome Bioinformatics Group, Santa Cruz, CA, USA - Tim Dreszer, Kate Rosenbloom, Hiram Clawson, Kayla Smith, Robert Kuhn, and Donna Karolchik. The guinea pig sequence is made freely available before scientific publication with the following understanding: The data may be freely downloaded, used in analyses, and repackaged in databases. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data (The Broad Institute) is properly acknowledged. The center producing the data reserves the right to publish the initial large-scale analyses of the data set, including large-scale identification of regions of evolutionary conservation and large-scale genomic assembly. Large-scale refers to regions with size on the order of a chromosome (that is, 30 Mb or more). Any redistribution of the data should carry this notice. |
Horse Genome
| The UCSC Horse Genome Browser displays the draft assembly of the horse (Equus caballus) genome from The Broad Institute. This assembly is provided with the following acknowledgements: Funding: The National Human Genome Research Institute Project Leadership: The Broad Institute, Cambridge, MA, USA Sequencing/Assembly: The Broad Institute, Cambridge, MA, USA BAC End Reads: University of Veterinary Medicine Hanover, Germany, and the Helmholtz Centre for Infection Research, Braunschweig, Germany UCSC Horse Genome Browser/Initial Annotations (equCab2): UCSC Genome Bioinformatics Group, Santa Cruz, CA, USA - Larry Meyer, Hiram Clawson, Pauline Fujita, Brooke Rhead, and Donna Karolchik UCSC Horse Genome Browser/Initial Annotations (equCab1): UCSC Genome Bioinformatics Group, Santa Cruz, CA, USA - Fan Hsu, Brooke Rhead, Robert Kuhn, Hiram Clawson, Angie Hinrichs, Kate Rosenbloom, and Donna Karolchik The horse sequence is made freely available before scientific publication with the following understanding: The data may be freely downloaded, used in analyses, and repackaged in databases. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data (The Broad Institute) is properly acknowledged. The center producing the data reserves the right to publish the initial large-scale analyses of the data set, including large-scale identification of regions of evolutionary conservation and large-scale genomic assembly. Large-scale refers to regions with size on the order of a chromosome (that is, 30 Mb or more). Any redistribution of the data should carry this notice. |
Panda Genome
| The panda assembly was provided by BGI-Shenzhen with the following acknowledgements: Sequencing/Assembly: The Beijing Genomics Institute at Shenzhen UCSC Panda (ailMel1) Genome Browser: Hiram Clawson, Ann Zweig, and Antonio Coelho. Initial Genome Browser Annotations: UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA The panda sequence is made freely available with the following understanding: The data may be freely downloaded, used in analyses, and repackaged in databases. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data (BGI-Shenzhen) is properly acknowledged. The center producing the data reserves the right to publish the initial large-scale analyses of the data set, including large-scale identification of regions of evolutionary conservation and large-scale genomic assembly. Large-scale refers to regions with size on the order of a chromosome (that is, 30 Mb or more). Any redistribution of the data should carry this notice. |
Pig Genome
| The pig assembly was provided by NCBI with the following acknowledgements: Sequencing/Assembly: The Swine Genome Sequencing Consortium and the Wellcome Trust Sanger Institute UCSC Pig (ailMel1) Genome Browser: Hiram Clawson, Brian Raney, Mark Diekhans, and Mary Goldman. Initial Genome Browser Annotations: UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA The pig sequence is made freely available with the following understanding: The data may be freely downloaded, used in analyses, and repackaged in databases. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data is properly acknowledged. The center producing the data reserves the right to publish the initial large-scale analyses of the data set, including large-scale identification of regions of evolutionary conservation and large-scale genomic assembly. Large-scale refers to regions with size on the order of a chromosome (that is, 30 Mb or more). Any redistribution of the data should carry this notice. |
Rabbit Genome
| The rabbit Genome Browser was produced with the following acknowledgements: Sequencing/Assembly: The Broad Institute at MIT and Harvard, Cambridge, MA, USA UCSC Rabbit (oryCun2) Genome Browser: Hiram Clawsom and Antonio Coelho Initial Genome Browser Annotations: UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA The rabbit sequence is made freely available before scientific publication with the following understanding: The data may be freely downloaded, used in analyses, and repackaged in databases. Users are free to use the data in scientific papers analyzing particular genes and regions if the providers of these data (the Broad Institute) are properly acknowledged. The centers producing the data reserve the right to publish the initial large-scale analyses of the data set, including large-scale identification of regions of evolutionary conservation and large-scale genomic assembly. Large-scale refers to regions with size on the order of a chromosome (that is, 30 Mb or more). Any redistribution of the data should carry this notice. |
Platypus Genome
| The platypus Genome Browser was produced with the following acknowledgements: Sequencing/Assembly: The Genome Sequencing Center at Washington University School of Medicine, St. Louis, MO, USA (WUSTL) UCSC Platypus (ornAna1) Genome Browser: Angie Hinrichs, Kayla Smith, Robert Kuhn, Brian Raney, and Donna Karolchik Initial Genome Browser Annotations: UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA The platypus sequence is made freely available before scientific publication with the following understanding: The data may be freely downloaded, used in analyses, and repackaged in databases. Users are free to use the data in scientific papers analyzing particular genes and regions if the providers of these data are properly acknowledged. See the WUSTL website for credit information. The centers producing the data reserve the right to publish the initial large-scale analyses of the data set, including large-scale identification of regions of evolutionary conservation and large-scale genomic assembly. Large-scale refers to regions with size on the order of a chromosome (that is, 30 Mb or more). This is in accordance with, and with the understandings in the Fort Lauderdale meeting discussing Community Resource Projects and the resulting NHGRI policy statement. Any redistribution of the data should carry this notice. |
Chicken Genome
| The chicken genome sequence was produced with the following acknowledgements: Sequencing: The Genome Sequencing Center at Washington University School of Medicine, St. Louis, MO, USA (WUSTL) Physical Map: WUSTL Genetic Mapping/Linkage Analysis: The Chicken Mapping Consortium: Wageningen Map based on Wageningen broilerxbroiler mapping population ("W" linkage maps; 460 F2 animals), coordinated by Martien Groenen, Wageningen University, Wageningen, The Netherlands East Lansing Map based on the RJFxlayer cross ("E" linkage maps; 56 BC animals), coordinated by Hans Cheng, USDA-ARS, East Lansing, MI, USA Compton map based on layerxlayer cross ("C" linkage maps; 52 BC animals), coordinated by Nat Bumstead, Institute for Animal Health Consensus linkage map: Martien Groenen and Richard Crooijmans, Wageningen University RH map: coordinated by Mireille Morisson and Alain Vignal, French National Institute for Agricultural Research (INRA), Toulouse (see the Chick RH Server) Linkage Mapping: White Leghorn X Red Junglefowl (800 F2 animals), coordinated by Susanne Kerje, Lina Jacobsson and Leif Andersson, Uppsala University, Uppsala, Sweden Clone/Marker Pairs: coordinated by Jerry Dodgson, Michigan State University, East Lansing, MI, USA Marker Name/Sequence Resolution: coordinated by Hans Cheng, USDA-ARS, East Lansing, MI, USA Chicken FPC browser: ChickFPC, Martien Groenen and Richard Crooijmans (galGal3), Jan Aerts (galGal2), Wageningen University Additional Mapping Data Contributions: Winston Bellott, David Page Lab, Whitehead Institute for Biomedical Research (WIBR-MIT), Cambridge, MA, USA cDNA sequences: National Institutes of Health and The University of Manchester BBSRC ChickEST Database RJF finished clones: NIH Intramural Sequencing Center (NISC) (AC091708.2, AC094012.2, AC138565.3) S. Kerje and L. Andersson, Uppsala University (AY636124.1) WUSTL (all others) Assembly, Assembly/Map Integration, Golden Path Creation: WUSTL SNPs and cross-referenced gene annotations: The Beijing Genomics Institute (BGI), Beijing, China UCSC Chicken Genome Browser (galGal3): Angie Hinrichs, Kayla Smith, Donna Karolchik UCSC Chicken Genome Browser (galGal2): Angie Hinrichs, Heather Trumbower, Rachel Harte, Donna Karolchik The G. gallus sequence is made freely available to the community by the Genome Sequencing Center, Washington University School of Medicine, with the following understanding: The data may be freely downloaded, used in analyses, and repackaged in databases. Users are free to use the data in scientific papers analyzing particular genes and regions if the providers of this data (Genome Sequencing Center, Washington University School of Medicine) are properly cited: International Chicken Genome Sequencing Consortium. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 2004 Dec 9;432(7018): 695-716. PMID: 15592404. Any redistribution of the data should carry this notice. The BGI gene annotations and SNP data are made available with the following terms of use: Users are free to use these data in scientific papers analyzing particular genes, if the Beijing Genomics Institute (BGI) is acknowledged. BGI and its collaborators reserve the right to publish the initial analyses of these data, including but not restricted to the large-scale identification of functional polymorphisms, evolutionary patterns and signs of selection, correlations with known QTLs, utility of data for genetic mapping purposes, etc. Any redistribution of these data should carry this notice. |
Turkey Genome
| The turkey Genome Browser was provided with the following acknowledgements: Sequencing/Assembly: The Turkey Genome Consortium - Virginia Tech College of Agriculture and Life Sciences and Virginia Bioinformatics Institute, Blacksburg, VA, USA UCSC Turkey (melGal1) Genome Browser: Chin Li, Mark Diekhans, Brian Raney, Brooke Rhead, Greg Roe, Steve Heitner, and Donna Karolchik Initial Genome Browser Annotations: UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA The turkey sequence is made freely available before scientific publication with the following understanding: The data may be freely downloaded, used in analyses, and repackaged in databases. Users are free to use the data in scientific papers analyzing particular genes and regions if the providers of these data (the Turkey Genome Consortium) are properly acknowledged. Any redistribution of the data should carry this notice. |
X. tropicalis Genome
| The X. tropicalis draft assemblies were provided by the U.S. DOE Joint Genome Institute (JGI). These assemblies have the following acknowledgements: Sequencing/Assembly: JGI, Walnut Creek, CA, USA UCSC X. tropicalis Genome Browser (xenTro3): Hiram Clawson, Brian Raney, Brooke Rhead, Greg Roe, Steve Heitner, and Donna Karolchik UCSC X. tropicalis Genome Browser (xenTro2): Angie Hinrichs, Kayla Smith, Robert Kuhn, and Donna Karolchik UCSC X. tropicalis Genome Browser (xenTro1): Fan Hsu, Jim Kent, Heather Trumbower, Hiram Clawson, Brian Raney, Galt Barber, Mark Diekhans, Angie Hinrichs, and Donna Karolchik Initial Annotations: UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA These sequence data are made freely available by the JGI. Please refer to the JGI data release policy for data use guidelines. |
Zebra Finch Genome
| The zebra finch draft assembly was obtained from the Genome Sequencing Center at Washington University St. Louis (WUSTL) School of Medicine with the following acknowledgements: Sequencing/Assembly: WUSTL, St. Louis, MO, USA Zebra finch DNA: Arthur P. Arnold lab, Dept. of Physiological Science, UCLA, Los Angeles, CA, USA UCSC Zebra Finch Genome Browser (taeGut1): Brian Raney, Kayla Smith, Pauline Fujita, and Donna Karolchik Initial Annotations: UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA The zebra finch sequence is made freely available to the community by the Genome Sequencing Center at the WUSTL School of Medicine with the following understanding: The data may be freely downloaded, used in analyses, and repackaged in databases. Users are free to use the data in scientific papers analyzing these data if the providers of these data are properly acknowledged. See http://genome.wustl.edu/data.cgi for credit information. The centers producing the data reserve the right to publish the initial large-scale analyses of the data set, including large-scale identification of regions of evolutionary conservation and large-scale genomic assembly. Large-scale refers to regions with size on the order of a chromosome. This is in accordance with, and with the understandings in the Fort Lauderdale meeting discussing Community Resource Projects and the resulting NHGRI policy statement. Any redistribution of the data should carry this notice. Please refer to the WUSTL data use policy for additional usage guidelines and citation information. |
Zebrafish Genome
| The zebrafish draft assemblies were provided by The Wellcome Trust Sanger Institute. The UCSC Zebrafish Genome Browser has the following acknowledgements: Sequencing/Assembly: The Wellcome Trust Sanger Institute, UK. FPC map: The Wellcome Trust Sanger Institute, UK Hubrecht Laboratory, Netherlands Institute for Developmental Biology, The Netherlands Max-Planck Institute for Developmental Biology, Germany BAC Clones, BAC End Pairs: The Wellcome Trust Sanger Institute, UK - GenBank accessions for BAC clones Max-Planck Institute for Developmental Biology, Germany - BAC end pairs sequence data Hubrecht Laboratory, Netherlands Institute for Developmental Biology, The Netherlands - BAC end pairs sequence data Initial Annotations: Yi Zhou, Anthony DiBiase, Leonard Zon and the Zebrafish Genome Initiative at Boston Children's Hospital, Boston, MA, US - collaboration on Zebrafish WZ EST clusters, BAC End Singles/Pairs, Radiation Hybrid, and Human tBLASTn annotation tracks. Washington University in St. Louis, St. Louis, MO, US - Zebrafish WZ EST clusters data Ensembl, UK - Ensembl gene predictions UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA - Other annotations UCSC Zebrafish Genome Browser (danRer7): Hiram Clawson, Mary Goldman, Greg Roe, Brian Raney, Donna Karolchik UCSC Zebrafish Genome Browser (danRer6): Galt Barber, Robert Kuhn, Katrina Learned, Donna Karolchik UCSC Zebrafish Genome Browser (danRer5): Rachel Harte, Ann Zweig, Donna Karolchik UCSC Zebrafish Genome Browser (danRer4): Rachel Harte, Archana Thakkapallayil, Robert Kuhn, Ann Zweig, Donna Karolchik UCSC Zebrafish Genome Browser (danRer3): Rachel Harte, Jennifer Jackson, Ann Zweig, Ali Sultan-Qurraie, Donna Karolchik UCSC Zebrafish Genome Browser (danRer2): Rachel Harte, Mark Diekhans, Heather Trumbower, Donna Karolchik, Jennifer Jackson These sequence data were produced by the Zebrafish Sequencing Group at the Sanger Institute and can be obtained directly from ftp://ftp.sanger.ac.uk/pub/zebrafish/. Please adhere to the data use guidelines for these data. For more information about the assemblies, see the Sanger Institute's Danio rerio Sequencing Project web page. |
Tetraodon Genome
| The Tetraodon nigroviridis assemblies have been provided with the following acknowledgements: Sequencing/Assembly: Genoscope, Evry, France The Broad Institute,MA, USA Project Funding: Consortium National de Recherche en Genomique, France National Human Genome Research Institute (NHGRI), USA Initial Genome Browser Annotations: Genoscope - Genscan gene predictions, GAZE gene predictions UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA - remaining annotations (based on data from Genoscope) UCSC Tetraodon (tetNig2) Genome Browser: Hiram Clawson, Mark Diekhans, Brian Raney, Ann Zweig, Mary Goldman, Vanessa Swing, Antonio Coelho, Robert Kuhn, and Donna Karolchik UCSC Tetraodon (tetNig1) Genome Browser: Rachel Harte, Robert Kuhn, Donna Karolchik These data have been freely provided by Genoscope before publication for use in the UCSC Genome Browser with the following understanding The data may be freely downloaded, used in analyses, and repackaged in databases. Users are free to use the data in scientific papers analyzing particular genes and regions, provided that the Genoscope is properly acknowledged. Genoscope reserves the right to publish the initial large-scale analyses of the dataset, including large-scale identification of regions of evolutionary conservation and large-scale genomic assembly. Large-scale refers to regions with size on the order of magnitude of a Tetraodon chromosome (that is, 5 Mb or more). |
Elephant Genome
| The elephant assembly was provided by the Broad Institute with the following acknowledgements: Sequencing/Assembly: The Broad Institute UCSC Elephant (loxAfr3) Genome Browser: Hiram Clawson, Pauline Fujita, Vanessa Swing, Antonio Coelho, and Donna Karolchik. Initial Genome Browser Annotations: UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA The elephant sequence is made freely available before scientific publication with the following understanding: The data may be freely downloaded, used in analyses, and repackaged in databases. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data (The Broad Institute) is properly acknowledged. The center producing the data reserves the right to publish the initial large-scale analyses of the data set, including large-scale identification of regions of evolutionary conservation and large-scale genomic assembly. Large-scale refers to regions with size on the order of a chromosome (that is, 30 Mb or more). Any redistribution of the data should carry this notice. |
Fugu Genome
| The Fugu whole genome shotgun assembly was provided by the U.S. 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). The assembly has the following acknowledgements: Sequencing/Assembly: Assembly was constructed with the JGI assembler, JAZZ, from paired end sequencing reads produced by JGI and the IMCB at JGI, Myriad Genetics, and Celera Genomics UCSC Fugu (fr2) Genome Browser: Cory McClean, Hiram Clawson, Ann Zweig, and Donna Karolchik UCSC Fugu (fr1) Genome Browser: Kate Rosenbloom, Heather Trumbower, Robert Kuhn, and Donna Karolchik Initial Genome Browser Annotations: UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA The Fugu sequence data have been freely provided by the JGI for use in the UCSC Genome Browser. Please see the JGI data release policy for restrictions regarding the use of these data. |
Lamprey Genome
| The lamprey assembly was provided by the Genome Sequencing Center at Washington University St. Louis (WUSTL) School of Medicine with the following acknowledgements: Funding: National Human Genome Research Institute (NHGRI) Sequencing/Assembly: WUSTL, St. Louis, MO, USA UCSC Lamprey (petMar1) Genome Browser: Hiram Clawson, Ann Zweig, Pauline Fujita, and Donna Karolchik Initial Genome Browser Annotations: UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA The lamprey sequence is made freely available before scientific publication. Please see the WUSTL data use policy for usage restrictions and citation information. |
Lancelet Genome
| The lancelet assembly was provided by the DOE Joint Genome Institute (JGI) with the following acknowledgements: Funding: U.S. Department of Energy Office of Science, Biological and Environmental Research Program Sequencing/Assembly: JGI UCSC Lancelet (braFlo1) Genome Browser: Hiram Clawson, Ann Zweig, Pauline Fujita, and Donna Karolchik Initial Genome Browser Annotations: UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA The lancelet sequence is made freely available before scientific publication by the JGI. Please see the JGI data release policy for usage restrictions and citation information. |
Lizard Genome
| The lizard assembly was provided by the Broad Institute with the following acknowledgements: Sequencing/Assembly: The Broad Institute UCSC Lizard (anoCar2) Genome Browser: Hiram Clawson, Brian Raney, Luvina Guruvadoo, and Donna Karolchik UCSC Lizard (anoCar1) Genome Browser: Hiram Clawson, Archana Thakkapallayil, Robert Kuhn, and Donna Karolchik Initial Genome Browser Annotations: UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA The lizard sequence is made freely available before scientific publication with the following understanding: The data may be freely downloaded, used in analyses, and repackaged in databases. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data (The Broad Institute) is properly acknowledged. The center producing the data reserves the right to publish the initial large-scale analyses of the data set, including large-scale identification of regions of evolutionary conservation and large-scale genomic assembly. Large-scale refers to regions with size on the order of a chromosome (that is, 30 Mb or more). Any redistribution of the data should carry this notice. |
Sheep Genome
| The sheep (Ovis aries) assembly was provided by the International Sheep Genomics Consortium (ISGC) sequencing center with the following acknowledgements: Sequencing/Assembly: International Sheep Genomics Consortium (ISGC) sequencing center Mitochondrial Genome Sequencing: Justus-Liebig-University UCSC Sheep (oviAri1) Genome Browser: Chin Li, Greg Roe, Luvina Guruvadoo Initial Genome Browser Annotations: UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA The sheep sequence is made freely available before scientific publication with the following understanding: The data may be freely downloaded, used in analyses, and repackaged in databases. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data (International Sheep Genomics Consortium) is properly acknowledged. The center producing the data reserves the right to publish the initial large-scale analyses of the data set, including large-scale identification of regions of evolutionary conservation and large-scale genomic assembly. Large-scale refers to regions with size on the order of a chromosome (that is, 30 Mb or more). Any redistribution of the data should carry this notice. |
Stickleback Genome
| The stickleback assembly was provided by the Broad Institute with the following acknowledgements: Sequencing/Assembly: The Broad Institute UCSC Stickleback (gasAcu1) Genome Browser: Angie Hinrichs, Hiram Clawson, Kayla Smith, and Donna Karolchik Initial Genome Browser Annotations: UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA The stickleback sequence is made freely available before scientific publication with the following understanding: The data may be freely downloaded, used in analyses, and repackaged in databases. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data (The Broad Institute) is properly acknowledged. The center producing the data reserves the right to publish the initial large-scale analyses of the data set, including large-scale identification of regions of evolutionary conservation and large-scale genomic assembly. Large-scale refers to regions with size on the order of a chromosome (that is, 30 Mb or more). Any redistribution of the data should carry this notice. |
Marmoset Genome
| These data were provided by the Genome Center at Washington University St. Louis (WUSTL) School of Medicine and the Human Genome Sequencing Center at the Baylor College of Medicine (BCM) with the following acknowledgements: Sequencing and assembly: Genome Center, WUSTL School of Medicine, St. Louis, MO, USA and Human Genome Sequencing Center, BCM, Houston, TX, USA DNA Source: Dr. Suzette Tardif, Southwestern National Primate Research Center, San Antonio, TX, USA CHORI-259 BAC library: Dr. Pieter DeJong, Children's Hospital Oakland Research Institute, Oakland, CA, USA UCSC Marmoset (calJac3) Genome Browser: Hiram Clawson, Chin Li, Mark Diekhans, Mary Goldman, Vanessa Swing, and Donna Karolchik UCSC Marmoset (calJac1) Genome Browser: Hiram Clawson, Robert Kuhn, Pauline Fujita, Brooke Rhead, and Donna Karolchik Initial Genome Browser Annotations: UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA These data were produced by the Genome Center at the WUSTL School of Medicine and the Human Genome Sequencing Center at the Baylor College of Medicine (BCM) and can be obtained from their downloads page. Please review the Genome Center's data use policy before using these data in publications. If you have any questions regarding the use of these data, please contact WUSTL at webmaster@genome.wustl.edu. |
Medaka Genome
| The Medaka whole genome shotgun assembly was provided by Japan's National Institute of Genetics (NIG) and the University of Tokyo. The assembly was constructed using the RAMEN assembler. NOTE: The UCSC oryLat1 assembly was replaced by oryLat2 in Nov. 2008 to correct a UCSC assembly error with chrUn in which the gap relationships between contigs within their ultracontigs were broken. The oryLat2 assembly is based on the same assembly as oryLat1: the v1.0 assembly from NIG and the University of Tokyo. Sequencing/Assembly: NIG and University of Tokyo, Japan UCSC Medaka (oryLat2) Genome Browser: Hiram Clawson, Pauline Fujita, and Donna Karolchik Initial Genome Browser Annotations: UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA The Medaka genome sequence data are made available to the public with certain restrictions. |
Microbat Genome
| The microbat (little brown bat) genome was provided by the The Broad Institute with the following acknowledgements: Sequencing/Assembly: The Broad Institute, Cambridge, MA, USA UCSC Microbat (myoLuc2) Genome Browser: Chin Li, Brian Raney, Robert Kuhn, Steve Heitner, Brooke Rhead, Greg Roe and Donna Karolchik Initial Genome Browser Annotations: UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA The microbat genome sequence data are made available to the public with the following understanding: The data may be freely downloaded, used in analyses, and repackaged in databases. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data (The Broad Institute) is properly acknowledged. The center producing the data reserves the right to publish the initial large-scale analyses of the data set, including large-scale identification of regions of evolutionary conservation and large-scale genomic assembly. Large-scale refers to regions with size on the order of a chromosome (that is, 30 Mb or more). Any redistribution of the data should carry this notice. |
C. Intestinalis Genome
| The C. intestinalis v1.0 and v2.0 draft assemblies were provided by the U.S. DOE Joint Genome Institute (JGI). These assemblies have the following acknowledgements, as listed on the JGI website: Project Funding: Work performed under the auspices of the US Department of Energy's Office of Science, Biological and Environmental Research Program and the by the University of California, Lawrence Livermore National Laboratory under Contract No. W-7405-Eng-48, Lawrence Berkeley National Laboratory under contract No. DE-AC03-76SF00098 and Los Alamos National Laboratory under contract No. W-7405-ENG-36. Project Collaborators: JGI, Walnut Creek, CA, USA Department of Zoology, Graduate School of Science, Kyoto University, Kyoto, Japan Department of Molecular and Cellular Biology, University of California, Berkeley, CA, USA National Institute of Genetics, Mishima, Japan Oak Ridge National Laboratory, Oak Ridge, TN, USA Los Alamos National Laboratory, Los Alamos, NM, USA Annotations: Colin Dewey, University of California, Berkeley, CA, USA - SNAP Gene Predictions, using the SNAP parser written by Ian Korf JGI, Walnut Creek, CA, USA - JGI Gene Predictions UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA - Other annotations UCSC C. intestinalis ci1 Genome Browser: Brian Raney, Galt Barber, Heather Trumbower, Robert Kuhn, Donna Karolchik UCSC C. intestinalis ci2 Genome Browser: Brian Raney, Mark Diekhans, Ann Zweig, Kayla Smith, Robert Kuhn, Donna Karolchik The sequence data have been freely provided by the JGI for use in the UCSC Genome Browser. The JGI Data Release Policy outlines restrictions on the use of these data. For more information about the C. intestinalis assembly, see the JGI Ciona web page. |
S. purpuratus Genome
| The UCSC S. purpuratus Genome Browser displays data obtained from the Baylor College of Medicine Human Genome Sequencing Center (BCM HGSC). The Sep. 2006 draft assembly shows data from Baylor version Spur 2.1; the Apr. 2005 assembly corresponds to Baylor version Spur_0.5. These data are provided with the following acknowledgements: Funding - National Human Genome Research Institute (NHGRI) Sequencing/Assembly: BCM HGSC, Houston, TX, USA UCSC S. purpuratus Genome Browser/Initial Annotations (strPur2): UCSC Genome Bioinformatics Group, Santa Cruz, CA, USA - Kord Kober, Heather Trumbower, Rachel Harte, Kayla Smith and Donna Karolchik. UCSC S. purpuratus Genome Browser/Initial Annotations (strPur1): UCSC Genome Bioinformatics Group, Santa Cruz, CA, USA - Andy Pohl, Kayla Smith and Donna Karolchik. For more information on the S. purpuratus genome project, see the BCM HGSC Sea Urchin Genome Project web page. To review the conditions for use regarding these data, see the BCM HGSC Conditions for Use web page. |
D. melanogaster Genome
| The D. melanogaster assemblies displayed in the UCSC Genome Browser were obtained from the Berkeley Drosophila Genome Project (BDGP) with the following acknowledgements: Sequencing and Assembly: Euchromatic sequence - BDGP, Berkeley, CA, USA Heterochromatic sequence - Drosophila Heterochromatin Genome Project, Lawrence Berkeley National Laboratory, Berkeley, CA, USA Annotations: Euchromatic regions - FlyBase Heterochromatic regions - DHGP, Lawrence Berkeley National Laboratory, Berkeley, CA, USA UCSC D. melanogaster (dm3) Genome Browser and additional annotations: Angie Hinrichs, Archana Thakkapallayil, Kayla Smith, and Donna Karolchik - UCSC Genome Bioinformatics Group, UCSC, Santa Cruz, CA, USA UCSC D. melanogaster (dm2) Genome Browser and additional annotations: Angie Hinrichs, Brian Raney, Galt Barber, and Donna Karolchik - UCSC Genome Bioinformatics Group, UCSC, Santa Cruz, CA, USA UCSC D. melanogaster (dm1) Genome Browser and additional annotations: Angie Hinrichs, Brian Raney, Heather Trumbower, Ali Sultan-Qurraie, and Donna Karolchik - UCSC Genome Bioinformatics Group, UCSC, Santa Cruz, CA, USA For additional information about these data, including citation guidelines, see the BDGP web site. |
D. ananassae Genome
| The droAna2 data were provided by Agencourt Bioscience Corporation. The droAna1 data were produced by the Institute for Genomic Research (TIGR). The D. ananassae Genome Browser has the following acknowledgements: Sequencing: Agencourt Bioscience Corporation, Beverly, MA, USA Assembly: Agencourt Bioscience Corporation, Beverly, MA, USA, using the Arachne assembler (droAna2) TIGR, Rockville, MD, USA, using an assembler produced by Celera (droAna1) UCSC D. ananassae (droAna2) Genome Browser: Angie Hinrichs, Brian Raney, Ann Zweig, Kayla Smith, and Donna Karolchik UCSC D. ananassae (droAna1) Genome Browser: Angie Hinrichs, Brian Raney, Heather Trumbower, Ali Sultan-Qurraie, and Donna Karolchik Initial Genome Browser Annotations: UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA These data have been freely provided by Agencourt Bioscience Corporation before publication for use in the UCSC Genome Browser with the following understanding: The data may be freely downloaded, used in analyses, and repackaged in databases. Users are free to use the data in scientific papers analyzing particular genes and regions, provided that the Agencourt is properly acknowledged. Agencourt reserves the right to publish the initial large-scale analyses of the dataset, including large-scale identification of regions of evolutionary conservation and large-scale genomic assembly. Any redistribution of the data should carry this notice. Please contact Douglas R. Smith at Agencourt with questions concerning these data. |
D. persimilis Genome
| The droPer1 assembly was provided by the Broad Institute with the following acknowledgements: Sequencing/Assembly: The Broad Institute UCSC D. persimilis (droPer1) Genome Browser: Angie Hinrichs, Kayla Smith, Robert Kuhn, Jennifer Jackson and Donna Karolchik Initial Genome Browser Annotations: UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA The D. persimilis sequence is made freely available before scientific publication with the following understanding: The data may be freely downloaded, used in analyses, and repackaged in databases. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data (The Broad Institute) is properly acknowledged. The center producing the data reserves the right to publish the initial large-scale analyses of the data set, including large-scale identification of regions of evolutionary conservation and large-scale genomic assembly. Large-scale refers to regions with size on the order of a chromosome (that is, 30 Mb or more). Any redistribution of the data should carry this notice. |
D. erecta Genome
| The droEre1 data were provided by Agencourt Bioscience Corporation. The D. erecta Genome Browser has the following acknowledgements: Sequencing and Assembly: Agencourt Bioscience Corporation, Beverly, MA, USA, using the Arachne assembler UCSC D. erecta (droEre1) Genome Browser: Angie Hinrichs, Brian Raney, Jennifer Jackson and Donna Karolchik Initial Genome Browser Annotations: UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA These data have been freely provided by Agencourt Bioscience Corporation before publication for use in the UCSC Genome Browser with the following understanding: The data may be freely downloaded, used in analyses, and repackaged in databases. Users are free to use the data in scientific papers analyzing particular genes and regions, provided that the Agencourt is properly acknowledged. Agencourt reserves the right to publish the initial large-scale analyses of the dataset, including large-scale identification of regions of evolutionary conservation and large-scale genomic assembly. Any redistribution of the data should carry this notice. Please contact Douglas R. Smith at Agencourt with questions concerning these data. |
D. simulans Genome
| These data were provided by the Genome Sequencing Center at Washington University St. Louis (WUSTL) School of Medicine with the following acknowledgements: Sequencing and assembly: Genome Sequencing Center, WUSTL School of Medicine UCSC D. simulans Genome Browser: Angie Hinrichs, Jennifer Jackson, Ali Sultan-Qurraie, Brian Raney and Donna Karolchik Initial Genome Browser Annotations: UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA The D. simulans sequence is made freely available before scientific publication by the Genome Sequencing Center, WUSTL with the following understanding: The data may be freely downloaded, used in analyses, and repackaged in databases. Users are free to use the data in scientific papers analyzing particular genes and regions if the providers of these data (Genome Sequencing Center, WUSTL School of Medicine) are properly acknowledged. The Drosophila simulans analysis group is aiming to publish an initial analysis of the D. simulans genome sequence in 2005 (submitted in early 2005) that will include descriptions of the assembly, genome landscape, comparative analysis and initial gene content. People who would like to coordinate other genome-wide analysis with this work should contact Richard K. Wilson, Genome Sequencing Center Director, Washington University School of Medicine. We welcome a coordinated approach to describing this community resource. Any redistribution of the data should carry this notice. |
D. sechellia Genome
| The droSec1 assembly was provided by the Broad Institute with the following acknowledgements: Sequencing/Assembly: The Broad Institute UCSC D. sechellia (droSec1) Genome Browser: Angie Hinrichs, Kayla Smith and Donna Karolchik Initial Genome Browser Annotations: UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA The D. sechellia sequence is made freely available before scientific publication with the following understanding: The data may be freely downloaded, used in analyses, and repackaged in databases. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data (The Broad Institute) is properly acknowledged. The center producing the data reserves the right to publish the initial large-scale analyses of the data set, including large-scale identification of regions of evolutionary conservation and large-scale genomic assembly. Large-scale refers to regions with size on the order of a chromosome (that is, 30 Mb or more). Any redistribution of the data should carry this notice. |
D. yakuba Genome
| These data were provided by the Genome Sequencing Center at Washington University (WUSTL) School of Medicine, St. Louis with the following acknowledgements: Funding: National Human Genome Research Institute (NHGRI) Sequencing, assembly and AGP creation: Genome Sequencing Center, WUSTL School of Medicine Initial Sequencing Proposal, Project Collaboration: David J. Begun and Charles H. Langley, University of California, Davis, CA, USA UCSC D. yakuba Genome Browser (droYak2): Angie Hinrichs, Jennifer Jackson and Donna Karolchik UCSC D. yakuba Genome Browser (droYak1): Angie Hinrichs, Michael Chalup and Donna Karolchik Initial Genome Browser Annotations: UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA The D. yakuba sequence is made freely available before scientific publication by the Genome Sequencing Center, WUSTL with the following understanding: The data may be freely downloaded, used in analyses, and repackaged in databases. Users are free to use the data in scientific papers analyzing particular genes and regions if the providers of these data (Genome Sequencing Center, WUSTL School of Medicine) are properly acknowledged. The Drosophila yakuba analysis group is aiming to publish an initial analysis of the D. yakuba genome sequence in 2005 (submitted in early 2005) that will include descriptions of the assembly, genome landscape, comparative analysis and initial gene content. People who would like to coordinate other genome-wide analysis with this work should contact Richard K. Wilson, Genome Sequencing Center Director, Washington University School of Medicine. We welcome a coordinated approach to describing this community resource. Any redistribution of the data should carry this notice. |
D. virilis Genome
| These data were produced by Agencourt Bioscience Corporation. The D. virilis Genome Browser has the following acknowledgements: Sequencing and Assembly: Agencourt Bioscience Corporation, Beverly, MA, USA, using the Arachne assembler Funding: National Human Genome Research Institute (NHGRI), USA UCSC D. virilis (droVir2) Genome Browser: Angie Hinrichs, Brian Raney, Jennifer Jackson and Donna Karolchik UCSC D. virilis (droVir1) Genome Browser: Angie Hinrichs, Brian Raney, Heather Trumbower, Robert Kuhn, Jennifer Jackson, and Donna Karolchik Initial Genome Browser Annotations: UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA These data have been freely provided by Agencourt Bioscience Corporation before publication for use in the UCSC Genome Browser with the following understanding: The data may be freely downloaded, used in analyses, and repackaged in databases. Users are free to use the data in scientific papers analyzing particular genes and regions, provided that the Agencourt is properly acknowledged. Agencourt reserves the right to publish the initial large-scale analyses of the dataset, including large-scale identification of regions of evolutionary conservation and large-scale genomic assembly. Any redistribution of the data should carry this notice. Please contact Douglas R. Smith at Agencourt with questions concerning these data. |
D. mojavensis Genome
| These data were produced by Agencourt Bioscience Corporation. The D. mojavensis Genome Browser has the following acknowledgements: Sequencing and Assembly: Agencourt Bioscience Corporation, Beverly, MA, USA, using the Arachne assembler Funding: National Human Genome Research Institute (NHGRI), USA UCSC D. mojavensis (droMoj2) Genome Browser: Angie Hinrichs, Brian Raney, Jennifer Jackson and Donna Karolchik UCSC D. mojavensis (droMoj1) Genome Browser: Angie Hinrichs, Brian Raney, Galt Barber and Donna Karolchik Initial Genome Browser Annotations: UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA These data have been freely provided by Agencourt Bioscience Corporation before publication for use in the UCSC Genome Browser with the following understanding: The data may be freely downloaded, used in analyses, and repackaged in databases. Users are free to use the data in scientific papers analyzing particular genes and regions, provided that the Agencourt is properly acknowledged. Agencourt reserves the right to publish the initial large-scale analyses of the dataset, including large-scale identification of regions of evolutionary conservation and large-scale genomic assembly. Any redistribution of the data should carry this notice. Please contact Douglas R. Smith at Agencourt with questions concerning these data. |
D. pseudoobscura Genome
| These data were produced by the Human Genome Sequencing Center (HGSC) at Baylor College of Medicine. The D. pseudoobscura Genome Browser has the following acknowledgements: Sequencing and Assembly: Baylor College of Medicine HGSC UCSC D. pseudoobscura (dp3) Genome Browser: Angie Hinrichs, Brian Raney, Jennifer Jackson and Donna Karolchik UCSC D. pseudoobscura (dp2) Genome Browser: Angie Hinrichs, Heather Trumbower, Robert Kuhn, Donna Karolchik Initial Genome Browser Annotations: UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA The D. pseudoobscura data are made available with specific conditions for use. |
D. grimshawi Genome
| The droGri data were provided by Agencourt Bioscience Corporation. The D. grimshawi Genome Browser has the following acknowledgements: Sequencing and Assembly: Agencourt Bioscience Corporation, Beverly, MA, USA, using the Arachne assembler UCSC D. grimshawi (droGri1) Genome Browser: Angie Hinrichs, Brian Raney, Jennifer Jackson, Kayla Smith and Donna Karolchik Initial Genome Browser Annotations: UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA These data have been freely provided by Agencourt Bioscience Corporation before publication for use in the UCSC Genome Browser with the following understanding: The data may be freely downloaded, used in analyses, and repackaged in databases. Users are free to use the data in scientific papers analyzing particular genes and regions, provided that the Agencourt is properly acknowledged. Agencourt reserves the right to publish the initial large-scale analyses of the dataset, including large-scale identification of regions of evolutionary conservation and large-scale genomic assembly. Any redistribution of the data should carry this notice. Please contact Douglas R. Smith at Agencourt with questions concerning these data. |
A. mellifera Genome
| The Amel_1.2 data were provided by The Baylor College of Medicine Human Genome Sequencing Center (BCM HGSC) with the following acknowledgements: Funding: National Human Genome Research Institute (NHGRI) and the U.S. Department of Agriculture (USDA) Sequencing and assembly: BCM HGSC, Houston, TX, USA BAC library: Pieter de Jong and Katzutoyo Osoegawa at Children's Hospital Oakland Research Institute (CHORI), Oakland, CA, USA UCSC A. mellifera (apiMel2) Genome Browser: Andy Pohl, Angie Hinrichs, Jennifer Jackson, and Donna Karolchik UCSC A. mellifera (apiMel1) Genome Browser: Angie Hinrichs, Brian Raney, Robert Kuhn, and Donna Karolchik Initial Genome Browser Annotations: UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA The A. mellifera sequence is made freely available before scientific publication by the BCM HGSC. See the Baylor conditions of use statement for guidelines regarding the use of these data. |
A. gambiae Genome
| The MOZ2 A. gambiae data were provided by The International Anopheles Genome Project and downloaded from Ensembl. The data have the following acknowledgements: Funding: National Institute of Allergy and Infectious Diseases (NIAID), French Ministry of Research, and the World Health Organization (WHO). Celera Genomics and Genoscope were funded respectively by National Institutes of Health (NIH) and French Ministry of Research. Project collaboration: The International Anopheles Genome Project - a collaboration between Celera Genomics, Genoscope, University of Notre Dame, EBI/Sanger Institute, EMBL, Institut Pasteur, The Institute of Molecular Biology and Biotechnology (IMBB) and The Institute for Genomic Research (TIGR). Sequencing and Assembly: Celera Genomics, Genoscope Data Downloads: Ensembl UCSC A. gambaie Genome Browser: Angie Hinrichs, Galt Barber and Donna Karolchik Initial Genome Browser Annotations: Ensembl and Celera Genomics (Ensembl Genes), the UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA (remaining annotations) The A. gambaie sequence is made freely available by The International Anopheles Genome Project. |
C. elegans Genome
| The C. elegans data was obtained from WormBase. We'd like to thank the Genome Sequencing Center at Washington University in St. Louis and the Sanger Institute for their collaborative work on sequencing the C. elegans genome, and the WormBase consortium for providing access to the current C. elegans sequence. |
Worm Genomes (other than C. elegans)
| The latest versions of the C. brenneri, C. briggsae, C. japonica, C. remanei, and P. pacificus sequences were obtained from the Genome Sequencing Center at Washington University in St. Louis (WUSTL) School of Medicine. The cb1 browser data were obtained from WormBase. Please review the WUSTL data use policy before using these data in research or a publication. We'd like to thank WUSTL for providing the sequence data for these assemblies, as well as the Sanger Institute for their collaborative work in sequencing the initial C. briggsae cb1 genome. Thanks also to the WormBase consortium for providing access to the cb1 sequence. |
Yeast Genome
| UCSC Sacchromyces cerevisiae Genome Browser (sacCer3): Hiram Clawson, Greg Roe, Steve Heitner. The April 2011 Sacchromyces cerevisiae genome assembly is based on sequence dated April 2011 in the Sacchromyces Genome Database (SGD). This genome sequence was downloaded from NCBI (genbank/genomes/Eukaryotes/fungi/Saccharomy ces_cerevisiae/SacCer_Apr2011/). The SGD™ gene annotations were downloaded from the SGD downloads site. The S288C strain was used in this sequencing project. The June 2008 Sacchromyces cerevisiae genome assembly is based on sequence dated June 2008 in the Sacchromyces Genome Database (SGD) and was obtained from the site http://downloads.yeastgenome.org/sequence/genomic_sequence/chromosomes/fasta/ The S288C strain was used in this sequencing project. The Oct. 2003 Sacchromyces cerevisiae genome assembly is based on sequence dated 1 Oct. 2003 in the Sacchromyces 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 cellular localization and protein abundance data displayed in the Gene Sorter are taken from the Yeast GFP Fusion Localization Database. See the SGD Systematic Sequencing Table for credit and contact information for each of the chromosomes in the assembly. We'd like to thank Stanford University, the SGD, the University of California San Francisco (UCSF), Washington University in St. Louis, and The Broad Institute for providing the data and annotations for this release. |
California Sea Hare Genome
| The Aplysia californica genome assembly has the following acknowledgements: Sequencing and Assembly: The Broad Institute, Cambridge, MA, USA UCSC California Sea Hare (aplCal1) Genome Browser: Galt Barber, Brian Raney, Hiram Clawson, Katrina Learned and Donna Karolchik Initial Genome Browser Annotations: UCSC Genome Bioinformatics Group, University of California, Santa Cruz, CA, USA The California sea hare sequence is made freely available before scientific publication with the following understanding: The data may be freely downloaded, used in analyses, and repackaged in databases. Users are free to use the data in scientific papers analyzing particular genes and regions if the provider of these data (The Broad Institute) is properly acknowledged. The center producing the data reserves the right to publish the initial large-scale analyses of the data set, including large-scale identification of regions of evolutionary conservation and large-scale genomic assembly. Large-scale refers to regions with size on the order of a chromosome (that is, 30 Mb or more). Any redistribution of the data should carry this notice. |
External Contributors to the UCSC Genome Browser Project
Affymetrix: Consensus and exemplar sequences for probe selection on several chips, exon array data, transcriptome data, Genie Gene predictions, design and analysis support in the early stages of the UCSC Human Genome project, including software for the synthetic chromosome 22 data we used to test our assembly methods. Agilent Technologies (Shane Giles, Peter Webb, and Dione Bailey): Agilent microarray probe sets. Allen Institute for Brain Science: Allen Brain Atlas probes. BAC Resource Consortium: Cytogenetic markers (FISH-mapped clones annotation track). Baylor College of Medicine (Richard Gibbs, John Bouck, Kim Worley and James Durbin): Rat Genome sequence data, D. pseudoobscura sequence for alignment tracks with D. melanogaster genome. Berkeley Drosophila Genome Project (BDGP): Data for D. melanogaster gene annotations. BioBase: Transfac database data used in HMR Conserved Transcription Factor Binding Sites track. Bioinformatics Solutions, Inc. (Ming Li and colleagues): Pattern Hunter mouse homology track. Biomarkers Consortium: I-SPY collaboration on the UCSC Cancer Genome Browser project. Biomedicinal Information Research Center (BIRC), National Institute of Advanced Industrial Science and Technology (AIST): H-InvDB Gene Predictions. Boston University (Tullius Lab, in collaboration with MIT, NHGRI, and the La Jolla Institute for Allergy and Immunology): ORChID Predicted DNA Cleavage Sites (ENCODE). The Broad Institute --(Eric Lander, Mike Zody, Chad Nusbaum): Plasmid end reads. Human working draft sequence analysis project. Special thanks to Eric for inviting us to join the Hardcore Analysis Group for the draft sequence project and for his direction of that group. --(Bernstein Lab): Histone modifications using ChIP-seq (ENCODE). California Institute of Technology (Wold Lab): RNA-Seq data (ENCODE). Canada's Michael Smith Genome Sciences Centre: ORegAnno data, brain DNA methylation track (ENCODE). Cedars-Sinai Medical Center (CSMC): FISH-mapped clones annotation track. Centre for Applied Genomics: Database of Genomic Variants (DGV) data. Centre d'Etude du Polymorphisme Humain (CEPH): Data from Genotype database for SNP Population Allele Frequencies track. Centre for Genomic Regulation (CRG) (Guigo Lab): CRG mapability (alignability) data, RNA-seq data. CNRS Université Paul Sabatier, Laboratoire de Biologie Moléculaire Eucaryote, Toulouse, France (Michel Weber): miRNA Data annotation track (in collaboration with Sam Griffiths-Jones of The Wellcome Trust Sanger Institute). Cold Spring Harbor Laboratory (CSHL) --(Stein Lab): HapMap data. --(Gingeras Lab and Hannon Lab): RNA-seq data tracks (ENCODE). --(Ivo Grosse and Michael Q. Zhang): Predictions for First Exon Finder annotation track. Consensus Coding Sequence Project (EBI, NCBI, WTSI, UCSC): Consensus CDS Genes. Cornell University (Siepel Lab): Exoniphy. Duke University (Institute for Genome Sciences and Policy): Open chromatin track, Human tissue Affymetrix Exon expression array data (ENCODE). EMBL (Peter Bork): Mouse pseudogene predictions used for Bork Pseudogenes custom annotation track. Emory University School of Medicine (D. Ledbetter, C. Martin): Collaboration on CGH-ICSA grant. Ensembl (Paul Flicek, Guy Slater, Imre Vastrik, Arek Kasprzyk, Michele Clamp): Ensembl Gene predictions, data exchange formats, TPF clone map coordination, exonerate mouse homology track, early help placing FISH-mapped clones. European Institute of Oncology: Nuclease accessible sites (ENCODE). FlyBase: Curated Drosophila gene annotations. Fred Hutchison Cancer Research Center (FHCRC) (Barbara Trask): FISH-mapped clones annotation track. Gene Ontology (GO) Consortium: Structured annotations for Gene Sorter. Genetic Information Research Institute (GIRI): Repbase repeat library, repeatmasking tools. Genome Informatics Research Lab (GIRL) within Grup de Recerca en Informàtica Mèdica (GRIB) (Francisco Câmara Ferreira, Roderic Guigó): Geneid and SGP gene prediction annotation tracks. Genomics Institute of the Novartis Research Foundation (GNF): Expression data using Affymetrix chips for GNF Expression Atlas annotation tracks. Genome Institute of Singapore (GIS): DNA Paired-end Ditag data, RNA-seq data (ENCODE). Genoscope (Jean Weissenbach and Olivier Jaillon): Exofish program, Tetraodon nigroviridis sequence for Tetraodon Blat alignments annotation tracks, data for Anopheles Evolutionary Conserved Regions annotation track. Helicos BioSciences: RNA-seq data (ENCODE). Hospital for Sick Children (Sick Kids) (L. Feuk): Structural variation data. HudsonAlpha Institute for Biotechnology (Myers Lab): RNA-seq data (ENCODE), Methyl-seq data (ENCODE), transcription factor binding sites identified by ChIP-seq (ENCODE), copy number variation (CNV) data (ENCODE). Illumnia: Probe set alignments. Institute for Genomic Research (TIGR): TIGR Gene Index annotation track. Institute for Systems Biology (Arian Smit): RepeatMasker repeat identification and masking software and libraries. International Knockout Mouse Consortium: Data for IKMC tracks. Iowa State University (J. Murray): Collaboration on FaceBase project. J. Craig Venter Institute: Nuclease accessible sites (ENCODE). Jackson Laboratory: Mouse Genome Informatics tracks, Mouse ortholog links from known genes track. Kyoto University, GenomeNet: Kyoto Encyclopedia of Genes and Genomes (KEGG) - pathway diagrams for Known Genes annotation track. Lawrence Berkeley National Laboratory (L.A. Pennacchio): Vista HMR-Conserved non-coding human enhancers track. Los Alamos National Laboratory (LANL): FISH-mapped clones annotation track. Massachusetts Institute of Technology (MIT) (Chris Burge): RNA-Seq data, Genscan gene prediction program. Medical College of Wisconsin: Rat Genome Database (RGD). Medical Research Council Laboratory of Molecular Biology: Superfamily database. Mount Sinai School of Medicine (Gary Benson - now at Boston University): Tandem Repeats Finder. National Cancer Institute (NCI), NIH: --The Cancer Genome Atlas (TCGA). --Mammalian Gene Collection (MGC) Project. --Cancer Genome Anatomy Project (CGAP). --SAGE project (in collaboration with NCBI). --FISH-mapped clones annotation track. National Center for Biotechnology Information (NCBI), NIH --RefSeq, Entrez Gene, dbSNP, HapMap, OMIM, and PubMed databases. --Serial Analysis of Gene Expression Tag to Gene Mapping (SAGEmap) data resource. --(Deanna Church): Mouse synteny track, database of whole genome shotgun mouse reads and assemblies used for mouse tracks. --(Greg Schuler): GenBank freezes of human clones used in the assembly, NT contigs of multiple finished clones, STS maps (in earlier freezes), specially-formatted versions of the finished chromosomes. --(Steve Sherry): SNP tracks. --(Wonhee Jang): FISH-mapped clones annotation track. --(Danielle and Jean Thierry-Mieg): Acembly Genes annotation track. --(Lukas Wagner): 3' EST track in the July 2000 browser. National Human Genome Research Institute (NHGRI), NIH --(Elnitski Lab): Bidirectional promoters, negative regulatory elements (ENCODE). --(ENCODE group): Guidance for ENCODE DCC, collaboration and contributions for various ENCODE annotation tracks. --GWAS: GWAS data from the Catalog of Published Genome-Wide Association Studies. --(NISC group): Collaboration and annotations for NISC browser, including curated gene annotations, DNAse I Hypersensitive Sites annotation, Multi-species Conserved Sequences (MCS) tracks, Binomial_25 Conservation Scores, ZooSeq Blastz alignments tracks. National Institute on Aging, NIH: Data from the Genetic Association Database. Netherlands Cancer Institute (van Steensel Lab): Nuclear lamina associated domains tracks. Ohio State University Bioinformatics & Computational Biology Group (Ramana V. Davuluri): Predictions for First Exon Finder annotation track. ORFeome Collaboration: ORFeome Collaboration human gene clones. Pennsylvania State University Center for Comparative Genomics and Bioinformatics: BLASTZ, LASTZ, and multiz alignment programs, Genome Alignment and Annotation Database (GALA), collaboration on multiple alignment annotation tracks, ENCODE annotation tracks, Personal Genome Variants track, Galaxy, regulatory potential scores tracks. Perlegen Sciences: STS markers for the Haplotype Blocks annotation track on chr 21, SNP data for the Affymetrix 120K SNP track, TNG radiation hybrid map. RIKEN Genomic Sciences Center: Chimpanzee BAC end sequence data, mouse annotations, human genome sequence contributions, CAGE tags RNA subcellular localization data (ENCODE). Roswell Park Cancer Institute (RPCI): FISH-mapped clones annotation track. SNP Consortium: Data for SNP annotation tracks. Softberry Inc. (V. Solovyev): Fgenesh++ and Fgenesv+ gene predictions, TSSW promoters tracks. Sperling Biomedical Foundation (Thomas Pringle): Technical consultant on Proteome Browser, avid Genome Browser user and the source of myriad ideas for expanding its functionality, early assistance and support for UCSC Genome Browser. Stanford University --(Bejerano Lab): GREAT tool. --(Morrison Institute for Population and Resource Studies, Human Genome Diversity Project): Data for SNP Population Allele Frequencies track. --SOURCE tool: SOURCE links from UCSC Genes tracks. Stanford University School of Medicine (Myers Lab - now at HudsonAlpha): Data set for Human Promoters custom annotation track. SwitchGear Genomics (N. Trinklein and S.F. Aldred): Transcription start sites (TSSs). UniProt: Protein data from UniProt database. Universidad de Granada, Grupo de Bioinformática, Spain (Jose L. Oliver): Isochore custom annotation track. University at Albany - SUNY (TenenBaum Lab): Target RNA binding protein expression measured by RIP-chip (ENCODE). University of CA, Berkeley (Lior Pachter, Simon Cawley, Marina Alexandersson): SLAM Gene predictions. University of CA, San Diego --(G. Yeo, now at Salk Institute): FOX2 adaptor-trimmed CLIP-seq reads track. --(Ren Lab, Ludwig Institute for Cancer Research): TAF1 binding in fibroblastoid cells assayed by ChIP-chip (ENCODE). University of CA, San Francisco: Collaboration on UCSC Cancer Browser, Chimera links from SNPs and UCSC Genes, FISH-mapped clones annotation track. --(ENCODE group): Brain DNA methylation track (ENCODE). University of CA, Santa Cruz --(R.E. Green): Neanderthal annotation tracks. --(Lowe Lab): tRNA Gene Predictions using tRNAscan-SE. University of Cambridge, Department of Oncology: Open chromatin track (ENCODE). University of Chicago (Pritchard Lab): Collaboration on Human Genome Diversity Project tracks. University of North Carolina, Chapel Hill (Lieb Lab): Open chromatin track (ENCODE). University of Pennsylvania (Y. Thomas Gan): Database of Transcribed Sequences (DoTS) Genes custom annotation track. University of Pittsburgh (M. Marazita): Collaboration on FaceBase project. University of Tennessee GeneNetwork: GeneNetwork links from UCSC Genes annotations. University of Texas Health Science Center, Greehy Children's Cancer Research Institute (L.O.F. Penalva): University of Texas, Austin (Iyer Lab): Open chromatin track (ENCODE). University of Vienna, Institute for Theoretical Chemistry and Structural Biology, Theoretical Biochemistry Group: Vienna RNA utility RNAplot - Known Genes annotation track. University of Washington --(Eichler Lab): Segmental duplications data. --(Human Genome Structural Variation Project): Variation data for HGSV tracks. --(ENCODE group): Digital DNase genomic footprinting track, DNaseI sensitivity using digital DNaseI methodology, DNaseI hypersensitive sites, histone modifications using ChIP-seq (ENCODE). --(Noble Lab): Predicted nucleosome occupancy tracks. --(Nickerson Lab): Tajima's D SNPs track. Uppsala University (Wadelius Lab): ChIP-chip data (ENCODE). Washington University in St. Louis and Washington University in St. Louis School of Medicine --(Robert Waterston (now at UW), John McPhearson, Asif Chinwalla, Shiaw-Pyng Yang, John Wallis and LaDeana Hillier): Fingerprint-based map of BAC clones from the human genome and a corresponding layout of sequenced clones, plasmid end reads, BACend analysis, CpG islands. --(Sean Eddy and Todd Lowe (now at UCSC)): RNA Genes track. --(Michael Brent Lab): N-SCAN and Twinscan Genes. --(ENCODE group): Brain DNA methylation track (ENCODE). Wellcome Trust Sanger Institute --(J. Harrow, J. Gilbert, J. Sulston, J. Rogers, J. Mullikin, R. Durbin, S. Searle, I. Dunham and the annotation teams): Vega Genes and Pseudogenes, Sanger 20 and Sanger 22 Genes and Pseudogenes. Plasmid end reads, processing of whole genome shotgun mouse reads. Eponine program. --(S. Griffiths-Jones): miRNA Data annotation track (in collaboration with M. Weber of CNRS Université Paul Sabatier). --Decipher --Protein Families Database of Alignments and HMMs (Pfam). Whitehead Institute, Bioinformatics and Research Computing (G. Bell): TargetScan miRNA regulatory sites. WormBase (Lincoln Stein): Wormbase curated gene annotations for C. elegans genome. Yale University: --(Snyder, Gerstein, and Weissman Labs in collaboration with NASA Ames Research Center and Eloret Corporation): Transcriptionally Active Regions (TARs) data (ENCODE). --(Sestan Lab): Exon microarray expression data from the late mid-fetal human brain. |
Acknowledgements of Early Support
| During the initial stage of this project, from January 2000 to June 2001, we received no direct federal funding to develop the working draft other than travel support. However, we gratefully acknowledge the support for our personnel provided by our basic bioinformatics research grants, especially DOE grant DE-FG03-99ER62849 (to develop gene-finding methods), but also NSF grant DBI-9809007, UC BIOTECH grant 99-11, a grant from the Sloan Foundation, the David and Lucille Packard Foundation, NIH grant GM-52848, and the Zahler grant that provided support for Jim Kent in the early stages of this work. We are particularly thankful for the risks that Patrick Mantey (UCSC Dean of Engineering), James Gill (Vice Chancellor for Research), John Simpson (UCSC Provost), and M.R.C. Greenwood (UCSC Chancellor) were willing to take in advancing us the money in February, 2000 needed to build the original 100-node LINUX cluster used in this work, and in the case of Dean Mantey, additional personnel support. Phokion Kolaitis, Chair of Computer Science, contributed as well. We thank Compaq for providing an additional 100-CPU computational cluster in Cambridge, MA for use by the public human genome effort. We thank ILOG, Inc. for providing discounted licenses to its CPLEX linear programming software, which was essential for some of our early experiments. Beginning in December, 2000, we started to utilize some support from HHMI for equipment and personnel. In the summer of 2001, HHMI provided the primary funding for a new cluster of 1000 CPUs running LINUX purchased from Rackable, with additional support from CISI and NHGRI. Dubbed the UCSC KiloKluster, this equipment now provides the computational backbone for the project. |