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

[william.j.burtle at gsk.com]

Joshua, 

you might also try the EMBOSS tools (particularly stretcher and needle): 
http://www.emboss.org/

and the bioperl interface: 
http://doc.bioperl.org/releases/bioperl-1.2/Bio/Factory/EMBOSS.html

- Bill Burtle







"Aaron J Mackey" <ajm6q at virginia.edu>

Sent by: bioperl-l-bounces at portal.open-bio.org
29-Aug-2003 07:41
Please respond to "Aaron J. Mackey" <amackey at virginia.edu>

 
 

        To:     "Joshua Bronson" <jbronson at acsu.buffalo.edu>

        cc:     "Bioperl list" <bioperl-l at bioperl.org>
        Subject:        Re: [Bioperl-l] aligning sequences with Bio::Tools::pSW


pSW.pm is an implementation of the Smith-Waterman algorithm, a *local*
pairwise alignment algorithm, which means that the best alignment found
need not start and finish at the beginning and ending of either sequence.
You seem to want a *global* alignment algorithm, such as Needleman-Wunsch
(with "free" end-gap penalties for globally aligning the larger sequence:
this is how to achieve hybrid local/global pairwise alignments); ClustalW
should be able to give you what you need.

-Aaron

On Thu, 28 Aug 2003, Joshua Bronson wrote:

> 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?
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>

-- 
 Aaron J Mackey
 Pearson Laboratory
 University of Virginia
 (434) 924-2821
 amackey at virginia.edu


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