[Bioperl-l] Remote tblastn against a sequenced genome at NCBI

Fairley, Derek Derek.Fairley at bll.n-i.nhs.uk
Fri Nov 10 05:15:52 EST 2006


Try the nabble.com mirror of this forum for easy searching of prior


-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org
[mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of
James.Rose at UCHSC.edu
Sent: 09 November 2006 22:56
To: bioperl-l at lists.open-bio.org
Subject: [Bioperl-l] Remote tblastn against a sequenced genome at NCBI

Hi- apologies if this subject has been addressed before, but I can't
seem to find a way to search prior threads short of downloading the
entire archives. I'm trying to use Bioperl to do something I thought
would be fairly simple:

Ingredients: one file containing a list of GI numbers for various

1) Read GI number from file.
2) run a remote tblastn search against the sequenced Spermophilus
tridecemlineatus genome with the GI number as query.
3) save resultant BLAST file to disk for later parsing.

As it stands, several hours of browsing and scripting has failed to turn
up anything that might be useful in this regard.

Any advice is very much appreciated.



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