[BiO BB] Obtaining Genomic Sequence
hjm at tacgi.com
Thu Mar 2 16:46:12 EST 2006
There was a thread on this less than a month ago on the bioperl list. CHeck
their archives around Feb 14th for a thread titled:
[Bioperl-l] Fetching genomic sequences based on HUGO names or GeneIDs
There are example scripts and docs available for this kind of activity now via
On Thursday 02 March 2006 10:45, Ryan Golhar wrote:
> Thanks for all your responses, but maybe I need to clarify what I'm
> trying to do. I have a list of accession #'s for genes. I want to get
> the full-length genomic sequences (including exons and introns).
> I can get the chromosome and genomic coordinates using NCBI's eutils
> efetch method, however I'm not sure how to retrieve part of a sequence.
> I don't see information on NCBI's eutils documentation and was wondering
> if anyone here knew.
> In other words, say I have a gene that occurs on human chromosome 1.
> The accession # of chr1 is NC_000001, and I have the genomic
> coordinates, say 100 to 5000 on the positive strand. Without retrieving
> the entire chromosome, how can I retrieve just bases 100 to 5000?
> I can't do this by hand, as I have 1500+ genes, so I'm hoping to perl
> script it...
> -----Original Message-----
> From: bio_bulletin_board-bounces+golharam=umdnj.edu at bioinformatics.org
> [mailto:bio_bulletin_board-bounces+golharam=umdnj.edu at bioinformatics.org
> ] On Behalf Of Ryan Golhar
> Sent: Thursday, March 02, 2006 1:02 AM
> To: 'The general forum at Bioinformatics.Org'
> Subject: [BiO BB] Obtaining Genomic Sequence
> If I have an accession # for a gene that I know occurs on a particular
> chromosome, how can I get the full genomic sequence for that gene
> containing all the exons and introns?
> Bioinformatics.Org general forum -
> BiO_Bulletin_Board at bioinformatics.org
> Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org
Harry J Mangalam - 949 856 2847 (vox; email for fax) - hjm at tacgi.com
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