[BiO BB] Obtaining Genomic Sequence

Ryan Golhar golharam at umdnj.edu
Thu Mar 2 13:45:28 EST 2006

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

More information about the BBB mailing list