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  Frequently Asked Questions: Assembly Releases and Versions
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  List of UCSC genome releases
 

Question:
"How do UCSC's release numbers correspond to those of other organizations, such as NCBI?"

Response:
Species UCSC Release Date Release Name Status
Humanhg17May 2004NCBI Build 35Available
 hg16Jul 2003NCBI Build 34Available
 hg15Apr 2003NCBI Build 33Available
 hg13Nov 2002NCBI Build 31Archived
 hg12Jun 2002NCBI Build 30Archived
 hg11Apr 2002NCBI Build 29Archived
 hg10Dec 2001NCBI Build 28Archived
 hg8Aug 2001UCSC-assembledArchived
 hg7Apr 2001UCSC-assembledArchived
 hg6Dec 2000UCSC-assembledArchived
 hg5Oct 2000UCSC-assembledArchived
 hg4Sep 2000UCSC-assembledArchived
 hg3Jul 2000UCSC-assembledArchived
 hg2Jun 2000UCSC-assembledArchived (no browser - data set only)
 hg1May 2000UCSC-assembledArchived (no browser - data set only)
ChimppanTro1Nov 2003CGSC Build 1 Version 1Available
DogcanFam1Jul 2004Broad Institute v1.0Available
Mousemm5May 2004NCBI Build 33Available
 mm4Oct 2003NCBI Build 32Available
 mm3Feb 2003NCBI Build 30Available
 mm2Feb 2002MGSCv3Archived
 mm1Nov 2001MGSCv2Archived
Ratrn3Jun 2003Baylor HGSC v3.1Available
 rn2Jan 2003Baylor HGSC v2.1Available
 rn1Nov 2002Baylor HGSC v1.0Archived
ChickengalGal2Feb 2004WUSTL Feb. 2004 releaseAvailable
X. tropicalisxenTro1Oct 2004JGI v.3.0Available
ZebrafishdanRer1Nov 2003Sanger Institute Zv3 Available
TetraodontetNig1Feb 2004Genoscope v7Available
Fugufr1Aug 2002JGI v3.0Available
C. intestinalisci1Dec. 2002JGI v1.0Available
D. melanogasterdm1Jan 2003BDGP Release 3.1Available
D. pseudoobscuradp2Aug 2003Baylor HGSC Freeze 1Available
D. yakubadroYak1Apr 2004WUSTL Release 1.0Available
A. gambiaeanoGam1Feb 2003IAGP v.MOZ2Available
C. elegansce2Mar 2004WormBase v. WS120Available
 ce1May 2003WormBase v. WS100Available
C. briggsaecb1Jul 2002WormBase v. cb25.agp8Available
YeastsacCer1Oct 2003SGD 1 Oct 2003 sequenceAvailable
SARSsc1Apr 2003GenBank sequence as of 14 Apr 2003Available
ZoozooJun 2002NISC Comp. Seq. Target 1Available



  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 UCSC and NCBI human assemblies differ?"

Response:
Recent UCSC and NCBI human assemblies (hg10 and higher) are identical.



  Differences between UCSC and NCBI mouse assemblies
 

Question:
"Is the UCSC mouse genome assembly 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 Monday - Saturday.
  • EST data: updated weekly on Saturday morning
  • Downloadable data files: updated weekly on Sunday 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.



  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.