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

[Joshua Bronson]

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?