• 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

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	fr3	Oct. 2011	JGI v5.0	Available
	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	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
Naked mole-rat	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	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
Wallaby	macEug2	Sep. 2009	Tammar Wallaby Genome Sequencing Consortium Meug_1.1	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

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

Question:
"What strain of mouse was used for the Mus musculus genome?"

Response:
C57BL/6J.

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.

1. The latest UniProt Knowledgebase (Release 46.0, Feb. 1st, 2005) was parsed and the results were stored in a newly created database sp050201.
2. A corresponding database, proteins050201, was constructed based on data in sp050201 and other protein data sources.
3. 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

5. 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.

6. 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.