Dear Greg, Thanks for your reply. I think I didn't make it clear in my previous email. I am not looking to get the sequence. I am looking for the alignment of a refseq sequence and the chromosome sequence from hg19. Is there a way to get the alignment in a text format like by clicking "Side by Side Alignment" in the left panel in the link I sent: http://genome.ucsc.edu/cgi-bin/hgc?g=htcCdnaAli&i=NM_000022&c=chr20&l=43248162&r=43280376&o=43248162&aliTable=refSeqAli&table=refGene Regards, Xiaomao
-----Original Message----- From: Greg Roe [mailto:[email protected]] Sent: Tuesday, February 21, 2012 4:08 PM To: Xiaomao Zhu Cc: [email protected] Subject: Re: [Genome] question on how to get the alignment of a refseq gene to genomic sequence Hi Xiaomao, You can get that using the table browser: http://genome.ucsc.edu/cgi-bin/hgTables Select hg19 then... group: Gene and Gene Pred Tracks track: RefSeq Genes table: refGene region: genome Next to identifiers click the paste list button, and paste in your list (i.e., NM_000022). Then select "sequence" for your output. - Greg On 2/20/12 12:47 PM, Xiaomao Zhu wrote: > Hi, > I'm interested in getting a text output format of the alignment of a refseq > gene (i.e., NM_000022) to hg19 genomic sequences, something like: > > http://genome.ucsc.edu/cgi-bin/hgc?g=htcCdnaAli&i=NM_000022&c=chr20&l= > 43248162&r=43280376&o=43248162&aliTable=refSeqAli&table=refGene > > Do you provide a tool or API to achieve that? > > Thanks. > > Xiaomao Zhu > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
