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

Chris Fields cjfields at uiuc.edu
Thu Nov 29 23:57:36 EST 2007


Bio::DB::EntrezGene and Bio::SeqIO::entrezgene are part of bioperl- 
core (I think they were added prior to the 1.5.1 release, but I'm not  
positive).  If possible you should try installing bioperl 1.5.2 or the  
latest code from CVS.

For directions on installing Bioperl for most OS's go here:

http://www.bioperl.org/wiki/Installing_BioPerl

 From CVS:

http://www.bioperl.org/wiki/Using_CVS

chris

On Nov 28, 2007, at 7:20 PM, Paul N. Hengen wrote:

>
> 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-Entrez-IDs-tf4894403.html#a14017289
> Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
>
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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