UCSC Genome Bioinformatics: FAQ

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:
The first release of an assembly is given a name using the first three characters of the organism's genus and species classification in the format gggSss#, with subsequent assemblies incrementing the number. Assemblies predating the 2003 introduction of the six-letter naming system were given two-letter names in a similar gs# format and human assemblies are named hg# for human genome.

SPECIES UCSC VERSION RELEASE DATE RELEASE NAME STATUS

MAMMALS

Human hg38 Dec. 2013 Genome Reference Consortium GRCh38 Available

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 (data only)

hg10 Dec. 2001 NCBI Build 28 Archived (data only)

hg8 Aug. 2001 UCSC-assembled Archived (data only)

hg7 Apr. 2001 UCSC-assembled Archived (data only)

hg6 Dec. 2000 UCSC-assembled Archived (data only)

hg5 Oct. 2000 UCSC-assembled Archived (data only)

hg4 Sep. 2000 UCSC-assembled Archived (data only)

hg3 Jul. 2000 UCSC-assembled Archived (data only)

hg2 Jun. 2000 UCSC-assembled Archived (data only)

hg1 May 2000 UCSC-assembled Archived (data only)

Alpaca vicPac2 Mar. 2013 Broad Institute Vicugna_pacos-2.0.1 Available

vicPac1 Jul. 2008 Broad Institute VicPac1.0 Available

Armadillo dasNov3 Dec. 2011 Broad Institute DasNov3 Available

Bushbaby otoGar3 Mar. 2011 Broad Institute OtoGar3 Available

Baboon papHam1 Nov. 2008 Baylor College of Medicine HGSC Pham_1.0 Available

papAnu2 Mar. 2012 Baylor College of Medicine Panu_2.0 Available

Cat felCat5 Sep. 2011 ICGSC Felis_catus-6.2 Available

felCat4 Dec. 2008 NHGRI catChrV17e Available

felCat3 Mar. 2006 Broad Institute Release 3 Available

Chimp panTro4 Feb. 2011 CGSC Build 2.1.4 Available

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

Chinese hamster criGri1 Jul. 2013 Beijing Genomics Institution-Shenzhen C_griseus_v1.0 Available

Cow bosTau7 Oct. 2011 Baylor College of Medicine HGSC Btau_4.6.1 Available

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 canFam3 Sep. 2011 Broad Institute v3.1 Available

canFam2 May 2005 Broad Institute v2.0 Available

canFam1 Jul. 2004 Broad Institute v1.0 Available

Dolphin turTru2 Oct. 2011 Baylor College of Medicine Ttru_1.4 Available

Elephant loxAfr3 Jul. 2009 Broad Institute LoxAfr3 Available

Ferret musFur1 Apr. 2011 Ferret Genome Sequencing Consortium MusPutFur1.0 Available

Gibbon nomLeu3 Oct. 2012 Gibbon Genome Sequencing Consortium Nleu3.0 Available

nomLeu2 Jun. 2011 Gibbon Genome Sequencing Consortium Nleu1.1 Available

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 Institute cavPor3 Available

Hedgehog eriEur2 May 2012 Broad Institute EriEur2.0 Available

eriEur1 Jun. 2006 Broad Institute Draft_v1 Available

Horse equCab2 Sep. 2007 Broad Institute EquCab2 Available

equCab1 Jan. 2007 Broad Institute EquCab1 Available

Kangaroo rat dipOrd1 Jul. 2008 Baylor/Broad Institute DipOrd1.0 Available

Manatee triMan1 Oct. 2011 Broad Institute TriManLat1.0 Available

Marmoset calJac3 Mar. 2009 WUSTL Callithrix_jacchus-v3.2 Available

calJac1 Jun. 2007 WUSTL Callithrix_jacchus-v2.0.2 Available

Megabat pteVam1 Jul. 2008 Broad Institute Ptevap1.0 Available

Microbat myoLuc2 Jul. 2010 Broad Institute MyoLuc2.0 Available

Minke whale balAcu1 Oct. 2013 KORDI BalAcu1.0 Available

Mouse mm10 Dec. 2011 Genome Reference Consortium GRCm38 Available

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 (data only)

Mouse lemur micMur1 Jul. 2007 Broad Institute MicMur1.0 Available

Naked mole-rat hetGla2 Jan. 2012 Broad Institute HetGla_female_1.0 Available

hetGla1 Jul. 2011 Beijing Genomics Institute HetGla_1.0 Available

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 susScr3 Aug. 2011 Swine Genome Sequencing Consortium Sscrofa10.2 Available

susScr2 Nov. 2009 Swine Genome Sequencing Consortium Sscrofa9.2 Available

Pika ochPri2 Jul. 2008 Broad Institute release OchPri2 Available

Platypus ornAna1 Mar. 2007 WUSTL v5.0.1 Available

Rabbit oryCun2 Apr. 2009 Broad Institute release OryCun2 Available

Rat rn5 Oct. 2011 RGSC Rnor_5.0 Available

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 rheMac3 Oct. 2010 Beijing Genomics Institute CR_1.0 Available

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

Rock hyrax proCap1 Jul. 2008 Baylor College of Medicine HGSC Procap1.0 Available

Sheep oviAri3 Aug. 2012 ISGC Oar_v3.1 Available

oviAri1 Feb. 2010 ISGC Ovis aries 1.0 Available

Shrew sorAra1 Jun. 2006 Broad Institute SorAra1.0 Available

Sloth choHof1 Jul. 2008 Broad Institute ChoHof1.0 Available

Squirrel speTri2 Nov. 2011 Broad Institute SpeTri2.0 Available

Squirrel monkey saiBol1 Oct. 2011 Broad Institute SaiBol1.0 Available

Tarsier tarSyr1 Aug. 2008 WUSTL/Broad Institute Tarsyr1.0 Available

Tasmanian devil sarHar1 Feb. 2011 Wellcome Trust Sanger Institute Devil_refv7.0 Available

Tenrec echTel2 Nov. 2012 Broad Institute EchTel2.0 Available

echTel1 Jul. 2005 Broad Institute echTel1 Available

Tree shrew tupBel1 Dec. 2006 Broad Institute Tupbel1.0 Available

Wallaby macEug2 Sep. 2009 Tammar Wallaby Genome Sequencing Consortium Meug_1.1 Available

White rhinoceros cerSim1 May 2012 Broad Institute CerSimSim1.0 Available

VERTEBRATES

American alligator allMis1 Aug. 2012 Int. Crocodilian Genomes Working Group allMis0.2 Available

Atlantic cod gadMor1 May 2010 Genofisk GadMor_May2010 Available

Budgerigar melUnd1 Sep. 2011 WUSTL v6.3 Available

Chicken galGal4 Nov. 2011 ICGC Gallus-gallus-4.0 Available

galGal3 May 2006 WUSTL Gallus-gallus-2.1 Available

galGal2 Feb. 2004 WUSTL Gallus-gallus-1.0 Available

Coelacanth latCha1 Aug. 2011 Broad Institute LatCha1 Available

Elephant shark calMil1 Dec. 2013 IMCB Callorhinchus_milli_6.1.3 Available

Fugu fr3 Oct. 2011 JGI v5.0 Available

fr2 Oct. 2004 JGI v4.0 Available

fr1 Aug. 2002 JGI v3.0 Available

Lamprey petMar2 Sep. 2010 WUGSC 7.0 Available

petMar1 Mar. 2007 WUSTL v3.0 Available

Lizard anoCar2 May 2010 Broad Institute AnoCar2 Available

anoCar1 Feb. 2007 Broad Institute AnoCar1 Available

Medaka oryLat2 Oct. 2005 NIG v1.0 Available

Medium ground finch geoFor1 Apr. 2012 BGI GeoFor_1.0 / NCBI 13302 Available

Nile tilapia oreNil2 Jan. 2011 Broad Institute Release OreNil1.1 Available

Painted turtle chrPic1 Dec. 2011 IPTGSC Chrysemys_picta_bellii-3.0.1 Available

Stickleback gasAcu1 Feb. 2006 Broad Institute 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 taeGut2 Feb. 2013 WUSTL v3.2.4 Available

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 Institute 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 ce10 Oct. 2010 WormBase v. WS220 Available

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 the data for older assemblies of the browser through our Downloads 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 hg#, panTro#, 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 SEARCHABLE PUBLIC Google Groups forum.

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

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
```
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
```
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 SEARCHABLE PUBLIC Google Groups forum.