Frequently Asked Questions: Assembly Releases and Versions

Topics

• 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

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List of UCSC genome releases

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

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.

Initial assembly release dates

When will the next assembly be out?

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

Where does UCSC obtain the assembly and annotation data displayed in the Genome Browser?

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

How do the human assemblies displayed in the UCSC Genome Browser differ from the NCBI human assemblies?

Recent human assemblies displayed in the Genome Browser (hg10 and higher) are identical to the NCBI assemblies.

Differences between UCSC and NCBI mouse assemblies

Is the mouse genome assembly displayed in the UCSC Genome Browser the same as the one on the NCBI website?

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

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?

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

How frequently does UCSC update its databases with new data from GenBank?

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 for human and mouse assemblies; updated approximately weekly for all other organisms
• 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

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?

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

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?

See the section on converting coordinates for information on assembly migration tools.

Missing annotation tracks

Why is my favorite annotation track missing from your latest release?

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?

Now that the human genome is "finished", will there be any more releases?

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

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

C57BL/6J.

UniProt (Swiss-Prot/TrEMBL) display changes

What has UCSC done to accommodate the changes to display IDs recently introduced by UniProt (aka Swiss-Prot/TrEMBL)?

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 SEARCHABLE, PUBLIC Google Groups forum.