Hi Chris, We don't store information in our tables in the format you are referring to: NM_XXXXXX.NN. We store NM_XXXXXX in the field labeled "acc" and NN in a field called "version" in the gbStatus table or gbCdnaInfo (which contains all the accessions in GenBank tracks (RefSeq, mRNAs, ESTs, human and non-human)) table.
If you are familiar with mysql you could use this example statement on our public MySql server to extract it in the format you are looking for: select concat(acc, ".", version) from gbCdnaInfo,refGene where acc = name; Here is information on how to access the public MySql server: http://genome.ucsc.edu/FAQ/FAQdownloads.html#download29 If you would prefer to use the table browser to extract this data, please see this previously answered mailing list question to get you started: https://lists.soe.ucsc.edu/pipermail/genome/2011-September/027099.html If you have further questions, please don't hesitate to contact the mailing list: [email protected]. Vanessa Kirkup Swing UCSC Genome Bioinformatics Group ---------- Forwarded message ---------- From: Chris Mitchell <[email protected]> Date: Wed, Oct 26, 2011 at 9:36 PM Subject: Re: [Genome] Refseq id with isoforms To: Luvina Guruvadoo <[email protected]> Cc: [email protected] Sorry I should have been more explicit. I'm trying to obtain the refseq id with the version number from the hg19 mysql database. I've looked in knowngene and refgene, and browsed through a few other tables without any luck. On Oct 26, 2011 6:04 PM, "Luvina Guruvadoo" <[email protected]> wrote: _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
