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

[Chris Fields]

Aaron, 

How well is Bio::Tools::pSW maintained?  I haven't seen many using it (most
tend to use the other alternatives you mention).

Chris

> -----Original Message-----
> From: aaron.j.mackey at gsk.com [mailto:aaron.j.mackey at gsk.com]
> Sent: Wednesday, August 09, 2006 12:43 PM
> To: Chris Fields
> Cc: bioperl-l at lists.open-bio.org; Prachi Shah
> Subject: Re: [Bioperl-l] Bio::Tools::pSW stop codon bug?
> 
> > 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