Hi Xiaomao, We don't have a specific tool or API to get the alignment. The sample page you provided a url for is what we have. You may be able to parse the url (e.g. the values set for c, r, o, aliTable , etc.) and write a tool to do screen scrapes of the alignments you need. However, as this isn't a real API, this isn't something we can provide any support on.
Also, please note our conditions of use say: " Program-driven use of this software is limited to a maximum of one hit every 15 seconds and no more than 5,000 hits per day." Please let us know if you have any additional questions: [email protected] - Greg Roe UCSC Genome Bioinformatics Group On 2/21/12 5:44 PM, Xiaomao Zhu wrote: > 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
