Hi Andrew, Sorry, we don't keep information about obsolete versions of GenBank cDNAs including RefSeq. We have a weekly automated process that downloads the latest info from GenBank and aligns the cDNA sequences to each reference genome assembly. So even assemblies that had obsoleted versions at some point shouldn't have them anymore, because the latest version has been aligned to them replacing the obsoleted version.
I looked up NM_005656 in Entrez Nucleotide (http://www.ncbi.nlm.nih.gov/nuccore/205360942) and the record contains this line: "On Sep 20, 2008 this sequence version replaced gi:14602458." hg19 dates to Feb. 2009, so it seems to me that NM_005656.2 would have appeared in hg18 before ~Sep 20-27, 2008 but never in hg19. NCBI gurus may be aware of an automated way to extract revision history from NCBI. Hope that helps, Angie ----- "Andrew Yee" <[email protected]> wrote: > From: "Andrew Yee" <[email protected]> > To: "Vanessa Kirkup Swing" <[email protected]> > Cc: [email protected] > Sent: Friday, October 1, 2010 8:52:34 PM GMT -08:00 US/Canada Pacific > Subject: Re: [Genome] determine if a reference sequence is Hg18 v. Hg19 > > 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 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
