[Bioperl-l] Bio::Tools::pSW stop codon bug?

[aaron.j.mackey at gsk.com]

> I personally don't use pSW much, but we at least can test what's 
> going on.  It may just be the way the local alignment behaves.  Maybe 
> the algorithm doesn't like end gaps!

by definition, local (as opposed to global) alignments don't have end 
gaps.

> > orf19.6264.3_old/1-162 
> > TSQLYTGLLIVAVPLGFLASPISTMMWLIGSSGVTVGAHA---------------AL
> > orf19.6264.3/1-177 
> > TSQLYTGLLIVAVPLGFLASPISTMMWLIGSSGVTVGAHAALMEKPIETVFEEEV*V

yes, this looks to be an alignment bug in pSW; if you remove the *, does 
the alignment end naturally at the AL?

is there some reason you are wedded to pSW as opposed to, say, bl2seq 
(BLAST-based pairwise alignment) or ssearch (SmithWaterman pairwise 
alignment) (both also accessible via BioPerl's SearchIO->HSP->AlignI 
pipeline)?

-Aaron