Hello Ray, Sequence data associated with CCDS and all of our other gene prediction tracks can be obtained using the table browser (http://www.genome.ucsc.edu/cgi-bin/hgTables). After selecting your assembly of interest select:
group: Genes and Gene Prediction Tracks track: CCDS table: ccdsGene region: genome (or you can specificy particular regions of interest) output format: sequence Then click on "get output". This will take you to a menu where you can select to retrieve introns, exons, UTRs and upstream/downstream regions. Hopefully this information was helpful and answers your question. If you have further questions or require clarification feel free to contact the mailing list at [email protected]. Regards, Pauline Fujita UCSC Genome Bioinformatics Group http://genome.ucsc.edu Cho, Raymond wrote: > Sorry to clarify, we are looking for each genomic protein coding sequence > with the flanking 5' and 3' sequence. > > This flanking sequence would therefore in some cases be intron, and in > others, UTR. > > Hope that makes it clearer. > > best, > Ray > > > -----Original Message----- > From: Cho, Raymond > Sent: Wed 2/11/2009 5:53 PM > To: [email protected] > Subject: CCDS sequence only + flanking genomic sequence > > Hello, I'm a researcher at UCSF attempting to download all the CCDS sequences > (human protein coding sequence) along with 200bp 5' and 3' of the genomic > flanking nucleotides for each sequence. > > What do you think the easiest way to get this data would be? > > Thank you for your hard work on this database! > > best, > Ray > > > _______________________________________________ > Genome maillist - [email protected] > http://www.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
