[Bioperl-l] Collecting genomic DNA sequences using Entrez IDs

Cook, Malcolm 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....


Malcolm Cook
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
> 
> 
> Hi.
> 
> 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.
> 
> --
> 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
> 
> --
> View this message in context: 
> http://www.nabble.com/Collecting-genomic-DNA-sequences-using-E
> ntrez-IDs-tf4894403.html#a14017289
> Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
> 
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