[BioPython] Parsing BLAST for ClustalW

[Michiel de Hoon]

Dear Alex,

Did you look at section 6.4 in the Biopython tutorial?

--Michiel.


--- On Thu, 8/21/08, Alex Garbino <agarbino at gmail.com> wrote:

> From: Alex Garbino <agarbino at gmail.com>
> Subject: [BioPython] Parsing BLAST for ClustalW
> To: biopython at lists.open-bio.org
> Date: Thursday, August 21, 2008, 1:44 AM
> Hello,
> 
> I'm a new python and biophython user.
> I'm trying to pull a BLAST result, parse it into a csv
> with the
> following fields:
> protein name, organism, common name, protein length, and
> FASTA sequence
> The goal is to then feed the fasta sequences into ClustalW
> (to do a
> phylogeny tree, look for conserved regions, etc).
> 
> I've managed to do the blast search, and parse the
> results into xml
> from python. However, I'm not sure how to grab the
> above information
> and put it together, so that I can save a csv and push it
> into
> clustalw.
> 
> Could someone help?
> 
> Thanks!
> Alex
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