Thanks for the reply. If I enter NM_005656.2 with the .2 verson number with either hg18 or hg19 assemblies, no matches come up. I was wondering if you can specify a ref seq with the extension (even though NM_005656.2 is now defunct) have the Genome Browser return which build the ref seq is associated with?
Thanks, Andrew On Thu, Sep 30, 2010 at 2:22 PM, Vanessa Kirkup Swing <[email protected]>wrote: > Hi Andrew, > > One of our engineers pointed out that you can also find a list for both the > hg18 and hg19 refseq names using our refgene table. An easy way to do this > is to use our table browser. > > To do this click on "Tables" from the blue navigation bar which will get > you to this page: http://genome.ucsc.edu/cgi-bin/hgTables > > Set the following: > clade: Mammal > genome: Human > assembly: hg18 or hg19 > group: Genes and Gene Prediction Tracks > track: RefSeq Genes > table: refgene > region: genome > output format: selected fields from primary and related tables > > Click on "get output" > > select "name" and other fields that might interest you. > > Click on "get output" > > Hope this helps. > > Vanessa Kirkup Swing > UCSC Genome Bioinformatics Group > > > ----- Original Message ----- > From: "Vanessa Kirkup Swing" <[email protected]> > To: "Andrew Yee" <[email protected]> > Cc: [email protected] > Sent: Thursday, September 30, 2010 10:04:50 AM GMT -08:00 US/Canada Pacific > Subject: Re: [Genome] determine if a reference sequence is Hg18 v. Hg19 > > Dear Andrew, > > The NCBI Reference Sequence NM_005656.2 is obsolete and therefore isn't > displayed anywhere on our browser. This sequence has been replaced in > genbank by version .3. > > Please feel free to contact the mailing list again if you have further > questions. > > Vanessa Kirkup Swing > UCSC Genome Bioinformatics Group > > > ----- Original Message ----- > From: "Andrew Yee" <[email protected]> > To: [email protected] > Sent: Wednesday, September 29, 2010 7:32:16 PM GMT -08:00 US/Canada Pacific > Subject: [Genome] determine if a reference sequence is Hg18 v. Hg19 > > Is there a way to query a table to determine which Hg build a sequence > belongs to? For example, take NCBI Reference Sequence NM_005656.2 (see > also http://www.ncbi.nlm.nih.gov/nuccore/14602458). I believe this > sequence > is Hg18. Is there a way to directly determine this by querying a table in > the Genome Browser? > > Thanks, > Andrew > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
