[Bioperl-l] GenBank subseq retrieval

[Chris Fields]

I'll give it a go today or tomorrow; since I'm working with WinXP it's a bit
more problematic (and using nmake to install works okay but doesn't work for
tests for some reason).  

In a nutshell, what I would like to do is get the region around a rnamotif
hit in the available microbial genomes, with annotation included, in order
to determine the genomic context of the hit.  It's tricky b/c each gi would
have a different start/stop for the sequences.  I could parse through each
genome file, maybe using GFF, but it should be possible getting the subseq
with annotation directly from GenBank using efetch.  

I'll toy around with it and suggest some things maybe to improve it.

Christopher Fields
Postdoctoral Researcher - Switzer Lab
Dept. of Biochemistry
University of Illinois Urbana-Champaign 
-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org] On Behalf Of Brian Osborne
Sent: Friday, December 16, 2005 10:42 PM
To: Chris Fields; bioperl-l
Subject: Re: [Bioperl-l] GenBank subseq retrieval

Chris,

Bug 1405, or enhancement 1405, is fixed. Try it out and see if it works for
you.

Brian O.


On 12/16/05 1:39 PM, "Chris Fields" <cjfields at uiuc.edu> wrote:

> I saw in Bugzilla that there was an attempt to add seq_start and seq_end
> (among other features) to Bio::DB::Genbank to allow subsequence retrieval
> through the efetch interface at NCBI:
> http://bugzilla.bioperl.org/show_bug.cgi?id=1405.
> 
> I didn't see the proposed updates in bioperl-live CVS.  Is this
implemented
> yet or is there an alternative way to do this w/o downloading the entire
> sequence?  I am parsing rnamotif hits from GenBank files to determine the
> genomic context of the region where the hit occurred.
> 
> Christopher Fields
> Postdoctoral Researcher - Switzer Lab
> Dept. of Biochemistry
> University of Illinois Urbana-Champaign
> 
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> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
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