Frequently Asked Questions: Assembly Releases and Versions
| List of UCSC genome releases Initial assembly release dates UCSC assemblies Comparison of UCSC and NCBI human assemblies Differences between UCSC and NCBI mouse assemblies Accessing older assembly versions Frequency of GenBank data updates Coordinate changes between assemblies Converting positions between assembly versions Missing annotation tracks What next with the human genome? Mouse strain used for mouse genome sequence UniProt (Swiss-Prot/TrEMBL) display changes Return to FAQ Table of Contents |
List of UCSC genome releases |
| Question: "How do UCSC's release numbers correspond to those of other organizations, such as NCBI?" Response:
SPECIES | UCSC VERSION | RELEASE DATE | RELEASE NAME | STATUS
VERTEBRATES |  |  |  |
Human | hg19 | Feb. 2009 | Genome Reference Consortium GRCh37 | Available
| hg18 | Mar. 2006 | NCBI Build 36.1 | Available
| hg17 | May 2004 | NCBI Build 35 | Available
| hg16 | Jul. 2003 | NCBI Build 34 | Available
| hg15 | Apr. 2003 | NCBI Build 33 | Archived
| hg13 | Nov. 2002 | NCBI Build 31 | Archived
| hg12 | Jun. 2002 | NCBI Build 30 | Archived
| hg11 | Apr. 2002 | NCBI Build 29 | Archived
| hg10 | Dec. 2001 | NCBI Build 28 | Archived
| hg8 | Aug. 2001 | UCSC-assembled | Archived
| hg7 | Apr. 2001 | UCSC-assembled | Archived
| hg6 | Dec. 2000 | UCSC-assembled | Archived
| hg5 | Oct. 2000 | UCSC-assembled | Archived
| hg4 | Sep. 2000 | UCSC-assembled | Archived
| hg3 | Jul. 2000 | UCSC-assembled | Archived
| hg2 | Jun. 2000 | UCSC-assembled | Archived (data set only)
| hg1 | May 2000 | UCSC-assembled | Archived (data set only)
Cat | felCat4 | Dec. 2008 | NHGRI catChrV17e | Available
| felCat3 | Mar. 2006 | Broad Institute Release 3 | Available
Chicken | galGal3 | May 2006 | WUSTL Gallus-gallus-2.1 | Available
| galGal2 | Feb. 2004 | WUSTL Gallus-gallus-1.0 | Available
Chimp | panTro3 | Oct. 2010 | CGSC Build 2.1.3 | Available
| panTro2 | Mar. 2006 | CGSC Build 2.1 | Available
| panTro1 | Nov. 2003 | CGSC Build 1.1 | Available
Cow | bosTau6 | Nov. 2009 | University of Maryland v3.1 | Available
| bosTau4 | Oct. 2007 | Baylor College of Medicine HGSC Btau_4.0 | Available
| bosTau3 | Aug. 2006 | Baylor College of Medicine HGSC Btau_3.1 | Available
| bosTau2 | Mar. 2005 | Baylor College of Medicine HGSC Btau_2.0 | Available
| bosTau1 | Sep. 2004 | Baylor College of Medicine HGSC Btau_1.0 | Archived
Dog | canFam2 | May 2005 | Broad Institute v2.0 | Available
| canFam1 | Jul. 2004 | Broad Institute v1.0 | Available
Elephant | loxAfr3 | Jul. 2009 | Broad loxAfr3 | Available
Fugu | fr2 | Oct. 2004 | JGI v4.0 | Available
| fr1 | Aug. 2002 | JGI v3.0 | Available
Gibbon | nomLeu1 | Jan. 2010 | Gibbon Genome Sequencing Consortium Nleu1.0 | Available
Gorilla | gorGor3 | May 2011 | Wellcome Trust Sanger Institute gorGor3.1 | Available
Guinea pig | cavPor3 | Feb. 2008 | Broad cavPor3 | Available
Horse | equCab2 | Sep. 2007 | Broad EquCab2 | Available
| equCab1 | Jan. 2007 | Broad EquCab1 | Available
Lamprey | petMar1 | Mar. 2007 | WUSTL v3.0 | Available
Lizard | anoCar2 | May 2010 | Broad AnoCar2 | Available
| anoCar1 | Feb. 2007 | Broad AnoCar1 | Available
Marmoset | calJac3 | Mar. 2009 | WUSTL Callithrix_jacchus-v3.2 | Available
| calJac1 | Jun. 2007 | WUSTL Callithrix_jacchus-v2.0.2 | Available
Medaka | oryLat2 | Oct. 2005 | NIG v1.0 | Available
Microbat | myoLuc2 | Jul. 2010 | Broad myoLuc2.0 | Available
Mouse | mm9 | Jul. 2007 | NCBI Build 37 | Available
| mm8 | Feb. 2006 | NCBI Build 36 | Available
| mm7 | Aug. 2005 | NCBI Build 35 | Available
| mm6 | Mar. 2005 | NCBI Build 34 | Archived
| mm5 | May 2004 | NCBI Build 33 | Archived
| mm4 | Oct. 2003 | NCBI Build 32 | Archived
| mm3 | Feb. 2003 | NCBI Build 30 | Archived
| mm2 | Feb. 2002 | MGSCv3 | Archived
| mm1 | Nov. 2001 | MGSCv2 | Archived
Opossum | monDom5 | Oct. 2006 | Broad Institute release MonDom5 | Available
| monDom4 | Jan. 2006 | Broad Institute release MonDom4 | Available
| monDom1 | Oct. 2004 | Broad Institute release MonDom1 | Available
Orangutan | ponAbe2 | Jul. 2007 | WUSTL Pongo_albelii-2.0.2 | Available
Panda | ailMel1 | Dec. 2009 | BGI-Shenzhen AilMel 1.0 | Available
Pig | susScr2 | Nov. 2009 | SGSC Sscrofa9.2 | Available
Platypus | ornAna1 | Mar. 2007 | WUSTL v5.0.1 | Available
Rabbit | oryCun2 | Apr. 2009 | Broad Institute release oryCun2 | Available
Rat | rn4 | Nov. 2004 | Baylor College of Medicine HGSC v3.4 | Available
| rn3 | Jun. 2003 | Baylor College of Medicine HGSC v3.1 | Available
| rn2 | Jan. 2003 | Baylor College of Medicine HGSC v2.1 | Archived
| rn1 | Nov. 2002 | Baylor College of Medicine HGSC v1.0 | Archived
Rhesus | rheMac2 | Jan. 2006 | Baylor College of Medicine HGSC v1.0 Mmul_051212 | Available
| rheMac1 | Jan. 2005 | Baylor College of Medicine HGSC Mmul_0.1 | Archived
Sheep | oviAri1 | Feb. 2010 | ISGC Ovis aries 1.0 | Available
Stickleback | gasAcu1 | Feb. 2006 | Broad Release 1.0 | Available
Tetraodon | tetNig2 | Mar. 2007 | Genoscope v7 | Available
| tetNig1 | Feb. 2004 | Genoscope v7 | Available
Turkey | melGal1 | Dec. 2009 | Turkey Genome Consortium v2.01 | Available
X. tropicalis | xenTro3 | Nov. 2009 | JGI v.4.2 | Available
| xenTro2 | Aug. 2005 | JGI v.4.1 | Available
| xenTro1 | Oct. 2004 | JGI v.3.0 | Available
Zebra finch | taeGut1 | Jul. 2008 | WUSTL v3.2.4 | Available
Zebrafish | danRer7 | Jul. 2010 | Sanger Institute Zv9 | Available
| danRer6 | Dec. 2008 | Sanger Institute Zv8 | Available
| danRer5 | Jul. 2007 | Sanger Institute Zv7 | Available
| danRer4 | Mar. 2006 | Sanger Institute Zv6 | Available
| danRer3 | May 2005 | Sanger Institute Zv5 | Available
| danRer2 | Jun. 2004 | Sanger Institute Zv4 | Archived
| danRer1 | Nov. 2003 | Sanger Institute Zv3 | Archived
DEUTEROSTOMES |  |  |  |
C. intestinalis | ci2 | Mar. 2005 | JGI v2.0 | Available
| ci1 | Dec. 2002 | JGI v1.0 | Available
Lancelet | braFlo1 | Mar. 2006 | JGI v1.0 | Available
S. purpuratus | strPur2 | Sep. 2006 | Baylor College of Medicine HGSC v. Spur 2.1 | Available
| strPur1 | Apr. 2005 | Baylor College of Medicine HGSC v. Spur_0.5 | Available
INSECTS |  |  |  |
A. mellifera | apiMel2 | Jan. 2005 | Baylor College of Medicine HGSC v.Amel_2.0 | Available
| apiMel1 | Jul. 2004 | Baylor College of Medicine HGSC v.Amel_1.2 | Available
A. gambiae | anoGam1 | Feb. 2003 | IAGP v.MOZ2 | Available
D. ananassae | droAna2 | Aug. 2005 | Agencourt Arachne release | Available
| droAna1 | Jul. 2004 | TIGR Celera release | Available
D. erecta | droEre1 | Aug. 2005 | Agencourt Arachne release | Available
D. grimshawi | droGri1 | Aug. 2005 | Agencourt Arachne release | Available
D. melanogaster | dm3 | Apr. 2006 | BDGP Release 5 | Available
D. melanogaster | dm2 | Apr. 2004 | BDGP Release 4 | Available
| dm1 | Jan. 2003 | BDGP Release 3 | Available
D. mojavensis | droMoj2 | Aug. 2005 | Agencourt Arachne release | Available
| droMoj1 | Aug. 2004 | Agencourt Arachne release | Available
D. persimilis | droPer1 | Oct. 2005 | Broad Institute release | Available
D. pseudoobscura | dp3 | Nov. 2004 | Flybase Release 1.0 | Available
| dp2 | Aug. 2003 | Baylor College of Medicine HGSC Freeze 1 | Available
D. sechellia | droSec1 | Oct. 2005 | Broad Release 1.0 | Available
D. simulans | droSim1 | Apr. 2005 | WUSTL Release 1.0 | Available
D. virilis | droVir2 | Aug. 2005 | Agencourt Arachne release | Available
| droVir1 | Jul. 2004 | Agencourt Arachne release | Available
D. yakuba | droYak2 | Nov. 2005 | WUSTL Release 2.0 | Available
| droYak1 | Apr. 2004 | WUSTL Release 1.0 | Available
NEMATODES |  |  |  |
C. brenneri | caePb2 | Feb. 2008 | WUSTL 6.0.1 | Available
| caePb1 | Jan. 2007 | WUSTL 4.0 | Available
C. briggsae | cb3 | Jan. 2007 | WUSTL Cb3 | Available
| cb1 | Jul. 2002 | WormBase v. cb25.agp8 | Available
C. elegans | ce6 | May 2008 | WormBase v. WS190 | Available
| ce4 | Jan. 2007 | WormBase v. WS170 | Available
| ce2 | Mar. 2004 | WormBase v. WS120 | Available
| ce1 | May 2003 | WormBase v. WS100 | Archived
C. japonica | caeJap1 | Mar. 2008 | WUSTL 3.0.2 | Available
C. remanei | caeRem3 | May 2007 | WUSTL 15.0.1 | Available
| caeRem2 | Mar. 2006 | WUSTL 1.0 | Available
P. pacificus | priPac1 | Feb. 2007 | WUSTL 5.0 | Available
OTHER |  |  |  |
Sea Hare | aplCal1 | Sep. 2008 | Broad Release Aplcal2.0 | Available
Yeast | sacCer3 | April 2011 | SGD April 2011 sequence | Available
| sacCer2 | June 2008 | SGD June 2008 sequence | Available
| sacCer1 | Oct. 2003 | SGD 1 Oct 2003 sequence | Available
Initial assembly release dates |
| Question: "When will the next assembly be out?" Response: UCSC does not produce its own genome assemblies, but instead obtains them from standard sources. For example, the human assembly is obtained from NCBI. Because of this, you can expect us to release a new version of a genome soon after the assembling organization has released the version. A new assembly release initially consists of the genome sequence and a small set of aligned annotation tracks. Additional annotation tracks are added as they are obtained or generated. Bulk downloads of the data are typically available in the first week after the assembly is released in the browser. |
Data sources - UCSC assemblies |
| Question: "Where does UCSC obtain the assembly and annotation data displayed in the Genome Browser?" Response: All the assembly data displayed in the UCSC Genome Browser are obtained from external sequencing centers. To determine the data source and version for a given assembly, see the assembly's description on the Genome Browser Gateway page or the List of UCSC Genome Releases. The annotations accompanying an assembly are obtained from a variety of sources. The UCSC Genome Bioinformatics Group generates several of the tracks; the remainder are contributed by collaborators at other sites. Each track has an associated description page that credits the authors of the annotation. For detailed information about the individuals and organizations who contributed to a specific assembly, see the Credits page. |
Comparison of UCSC and NCBI human assemblies |
| Question: "How do the human assemblies displayed in the UCSC Genome Browser differ from the NCBI human assemblies? Response: Recent human assemblies displayed in the Genome Browser (hg10 and higher) are identical to the NCBI assemblies. |
Differences between UCSC and NCBI mouse assemblies |
| Question: "Is the mouse genome assembly displayed in the UCSC Genome Browser the same as the one on the NCBI website?" Response: The mouse genome assemblies featured in the UCSC Genome Browser are the same as those on the NCBI web site with one difference: the UCSC versions contain only the reference strain data (C57BL/6J). NCBI provides data for several additional strains in their builds. |
Accessing older assembly versions |
| Question: "I need to access an older version of a genome assembly that's no longer listed in the Genome Browser menu. What should I do?" Response: In addition to the assembly versions currently available in the Genome Browser, you can access older versions of the browser through our archives. To view an older version, click the Archives link on the Genome Browser home page. |
Frequency of GenBank data updates |
| Question: "How frequently does UCSC update its databases with new data from GenBank?" Response: Daily and weekly incremental updates of mRNA, RefSeq, and EST data are in place for several of the more recent Genome Browser assemblies. Assemblies that are not on an incremental update schedule are updated whenever we load a new assembly or make a major revision to a table. Data are updated on the following schedule: Native and xeno mRNA and refSeq tracks: updated daily EST data: updated weekly on Saturday morning Downloadable data files: updated weekly on Saturday morning Outdated sequences - removed once per quarter Mirror sites are not required to use an incremental update process, and should not experience problems as a result of these updates. |
Coordinate changes between assemblies |
| Question: "I noticed that the chromosomal coordinates for a particular gene that I'm looking at have changed since the last time I used your browser. What happened?" Response: A common source of confusion for users arises from mixing up different assemblies. It is very important to be aware of which assembly you are looking at. Within the Genome Browser display, assemblies are labeled by organism and date. To look up the corresponding UCSC database name or NCBI build number, use the release table. UCSC database labels are of the form hgn, panTron, etc. The letters designate the organism, e.g. hg for human genome or panTro for Pan troglodytes. The number denotes the UCSC assembly version for that organism. For example, ce1 refers to the first UCSC assembly of the C. elegans genome. The coordinates of your favorite gene in one assembly may not be the same as those in the next release of the assembly unless the gene happens to lie on a completely sequenced and unrevised chromosome. For information on integrating data from one assembly into another, see the Converting positions between assembly versions section. |
Converting positions between assembly versions |
| Question: "I've been researching a specific area of the human genome on the current assembly, and now you've just released a new version. Is there an easy way to locate my area of interest on the new assembly?" Response: See the section on converting coordinates for information on assembly migration tools. |
Missing annotation tracks |
| Question: "Why is my favorite annotation track missing from your latest release?" Response: The initial release of a new genome assembly typically contains a small subset of core annotation tracks. New tracks are added as they are generated. In many cases, our annotation tracks are contributed by scientists not affiliated with UCSC who must first obtain the sequence, repeatmasked data, etc. before they can produce their tracks. If you have need of an annotation that has not appeared on an assembly within a month or so of its release, feel free to send an inquiry to genome@soe.ucsc.edu. Messages sent to this address will be posted to the moderated genome mailing list, which is archived on a public Web-accessible pipermail archive. This archive may be indexed by non-UCSC sites such as Google. |
What next with the human genome? |
| Question: "Now that the human genome is "finished", will there be any more releases?" Response: Rest assured that work will continue. There will be updates to the assembly over the next several years. This has been the case for all other finished (i.e. essentially complete) genome assemblies as gaps are closed. For example, the C. elegans genome has been "finished" for several years, but small bits of sequence are still being added and corrections are being made. NCBI will continue to coordinate the human genome assemblies in collaboration with the individual chromosome coordinators, and UCSC will continue to QC the assembly in conjunction with NCBI (and, to a lesser extent, Ensembl). UCSC, NCBI, Ensembl, and others will display the new releases on their sites as they become available. |
Mouse strain used for mouse genome sequence |
| Question: "What strain of mouse was used for the Mus musculus genome?" Response: C57BL/6J. |
UniProt (Swiss-Prot/TrEMBL) display changes |
3. | Question: "What has UCSC done to accommodate the changes to display IDs recently introduced by UniProt (aka Swiss-Prot/TrEMBL)?" Response: Here is a detailed description of the database changes we have made to accommodate the UniProt changes. If you are using the proteinID field in our knownGene table or the Swiss-Prot/TrEMBL display ID for indexing or cross-referencing other data, we strongly suggest you transition to the UniProt accession number. These changes will also affect anyone who is mirroring our site. The latest UniProt Knowledgebase (Release 46.0, Feb. 1st, 2005) was parsed and the results were stored in a newly created database sp050201. A corresponding database, proteins050201, was constructed based on data in sp050201 and other protein data sources. Two new symbolic database pointers, uniProt and proteome, have been created to point to the two new databases mentioned above. Some parts of our programs use the data in these two DBs.
          uniProt  ---> sp050201
          proteome ---> proteins050201
4. The existing protein symbolic database pointers, swissProt and proteins remain unchanged. Some parts of our programs still use these two pointers and the data in their associated protein databases.
          swissProt ---> sp041115
          proteins  ---> proteins041115
6. Two new tables, spOldNew and uniProtAlias, have been added to the proteome database. The spOldNew table contains three columns: acc -- primary accession number oldDisplayId -- old display ID newDisplayId -- new display ID The uniProtAlias table contains four columns: acc -- UniProt accession number alias -- alias (could be acc, old and new display IDs, etc.) aliasSrc -- source of the alias type aliasSrcDate -- date of the source data The aliases include primary accessions, secondary accessions new display IDs, old display IDs, and old display IDs corresponding to new secondary accessions. Three new functions have been added to kent/src/hg/spDb.c:
          char *oldSpDisplayId(char *newSpDisplayId);
          /* Convert from new Swiss-Prot display ID to old display ID */

          char *newSpDisplayId(char *oldSpDisplayId);
          /* Convert from old Swiss-Prot display ID to new display ID */

          char *uniProtFindPrimAcc(char *id);
          /* Return primary accession given an alias. */
The uniProtFindPrimAcc() function is enabled by the new uniProtAlias table. We anticipate additional changes down the road and may eventually merge the two sets of protein DB pointers into one set. Currently, the proteinID field of the knownGene table for existing genome releases (hg15, hg16, hg17, mm3, mm4, mm5, rn2, and rn3) uses old Swiss-Prot/TrEMBL display IDs (pre-1 Feb. '05). In the future, we may change this field to show the UniProt accession number. Should we choose not to change the content of the proteinID field, we may consider adding a new field, uniProtAcc. If you have any questions about these changes and their impact on your work, please email us at genome@soe.ucsc.edu. Mirror sites may send questions to genome-mirror@soe.ucsc.edu. Messages sent to these addresses will be posted to the moderated mailing lists, which are archived on a public Web-accessible pipermail archive. This archive may be indexed by non-UCSC sites such as Google. |