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

[Shawn Hoon]

On Friday, August 29, 2003, at 6:36 AM, 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?
>
We actually support these alignment programs as wrappers in the 
bioperl-run package.
We currently have Clustalw, Lagan, Fasta and TCoffee which you can try 
under the
Bio::Tools::Run::Alignment::* namespace.
>

bioperl-run 1.2.2 available here:

http://www.bioperl.org/DIST/current_run_stable.tar.gz

shawn

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>
-shawn