[BiO BB] Obtaining Genomic Sequence

[Harry Mangalam]

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 
their wiki.

hjm


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?
>
>
> Ryan
>
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-- 
Cheers, Harry
Harry J Mangalam - 949 856 2847 (vox; email for fax) - hjm at tacgi.com 
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