[Bioperl-l] Point me in the right direction--chromosomal positions

Sean Davis sdavis2 at mail.nih.gov
Mon Nov 22 21:08:43 EST 2004


What organism?  What are you looking up--refseq, genbank, gene names, 
locuslink?  I would suggest you use the table browser at UCSC 
(http://genome.ucsc.edu) or EnsMART (http://www.ensembl.org) unless there is 
some reason those won't work.  Bioperl doesn't have a mechanism to retrieve 
locations directly, at least that I know of (aside from DAS).  You can build 
databases to do help with that, but that is a bit of work for a problem with 
an existing solution.  You could also look into the EnsEMBL API.

Let me know if I can help with using those web interfaces.


----- Original Message ----- 
From: "Tomso, Dan (NIH/NIEHS)" <tomso at niehs.nih.gov>
To: <bioperl-l at bioperl.org>
Sent: Monday, November 22, 2004 11:00 AM
Subject: [Bioperl-l] Point me in the right direction--chromosomal positions

> Greetings all.
> I need a pointer-I'd like to retrieve gene names, start positions, end
> positions, orientations (strand), names, and descriptions via BioPerl.
> Can
> someone suggest the correct module, so I can digest the documentation?
> Thanks,
> Dan T.


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