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

[Aaron J Mackey]

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