[Bioperl-l] aligning sequences with Bio::Tools::pSW

[Brian Osborne]

Joshua,

> Bioperl doesn't seem to have an interface to do pairwise alignments with
Clustalw,

Bioperl is exactly what you want! See section IV.2.3 of the bptutorial,
"Aligning multiple sequences (Clustalw.pm, TCoffee.pm)". With the resulting
SimpleAlign object you'll have all sorts of useful methods for analyzing and
"slicing" the alignment.

Brian O.


-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Joshua Bronson
Sent: Thursday, August 28, 2003 6:37 PM
To: Bioperl list
Subject: [Bioperl-l] aligning sequences with Bio::Tools::pSW

I'm interested in the a portion of some virus polyproteins. To find
the portion, I'm aligning the polyprotein against other known
proteins. I want the computer to give me a best guess and align the
smaller protein end-to-end, but currently it's not doing that. It will
only give me portions of the protein that align strongly. None of the
proteins are aligning end-to-end, unless I align a protein against
itself.

Bio::Tools:pSW is what I'm using currently. Bioperl doesn't seem to
have an interface to do pairwise alignments with Clustalw, and I'm
experiencing problems using standalone blast. Anyone have any ideas?
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