Database versions for transcript databases?

[Vinayak Kulkarni]

Dear UCSC folks,

I query data from UCSC tables to do my analysis, once every 2 months. I look at a bunch of species (Hs, Mm, Rn ....) and mutliple datasources (Refseq, Ensembl, CCDS, Vega etc).

How do I know their database versions ? Example : RefSeq 151 and Ensembl 59 for Human data

Is there a table which houses this information? 

Thank you very much,

Vinayak.

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"Hesitating to act because the whole vision might  not be achieved, or because others do not yet share it, is an attitude that  only hinders
progress"... Mahatma Gandhi

[Greg Roe]

Hi, Vinayak.

There's no simple answer ... here's a breakdown for the gene sets you mentioned:

Some (Ensembl, Vega) of the info is in the db.table 'hgFixed.trackVersion' which can be accessed via MySQL: http://genome.ucsc.edu/goldenPath/help/mysql.html

For RefSeq genes, see this discussion: https://groups.google.com/a/soe.ucsc.edu/forum/#!topic/genome/ClmwZbanI_g/discussion

Vega: Look in hgFixed.trackVersion or click on a Vega gene in the Genome Browser. (Note that Vega is actually a subset of Ensembl and Gencode (Gencode is human only) that is manually annotated. They should state somewhere on their site which version of Vega is equal to which version of the other dbs: http://vega.sanger.ac.uk/index.html)

Ensembl: Look in hgFixed.trackVersion or view the track description in the Genome Browser.

CCDS: These are updated, I believe, once every 6 months by us. I don't think we store a version number for this one, but if you go to the track description page, we do list the date it was last updated. (Note, on the track description page it says, "CDS annotations of the human genome were obtained from two sources: NCBI RefSeq and a union of the gene annotations from Ensembl and Vega, collectively known as Hinxton.")

For any other ones that you may not have mentioned, the best place to start is on the track description page.

Please let us know if you have any additional questions: gen...@soe.ucsc.edu

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Greg Roe
UCSC Genome Bioinformatics Group

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