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
