[Bioperl-l] Collecting genomic DNA sequences using Entrez IDs
MEC at stowers-institute.org
Fri Nov 30 09:12:09 EST 2007
How many, how often?
Use ensembl biomart!
First time interactively.
Then if you to pipeline it, take the perl code it generates for you and
run it - of course you'll have to install the Ensembl Perl API....
Database Applications Manager - Bioinformatics
Stowers Institute for Medical Research - Kansas City, Missouri
> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org
> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of
> Paul N. Hengen
> Sent: Wednesday, November 28, 2007 7:21 PM
> To: Bioperl-l at lists.open-bio.org
> Subject: [Bioperl-l] Collecting genomic DNA sequences using Entrez IDs
> I have a number of gene IDs from Entrez and I want to find
> the start and end locations in the human genome. This seemed
> simple enough, so I started working through some of the
> examples for using the EntrezGene module at www.bioperl.org
> Of course this did not work because the core installation
> does not include this module. So, I think I have two choices
> (1) install the module (how?), or (2) find an easier way to
> get the locations in the human genome.
> I want to use the locations to grab sequences out of the genome.
> Can anyone offer advice on this? Thanks.
> Paul N. Hengen, Ph.D.
> Hematopoietic Stem Cell and Leukemia Research City of Hope
> National Medical Center 1500 E. Duarte Road, Duarte, CA 91010
> USA mailto:paulhengen at coh.org
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