[Bioperl-l] pSM vs .Framesearch

[Paul Gordon]

On Thu, 23 Aug 2001, Wiepert, Mathieu wrote:
> I had a question about pSM.  I have been using Framesearch, GCG's
> Smith-Waterman implementation, to compare a bunch of sequences against a
> bunch of contigs.  I wanted to not use GCG.  Does anyone know if there are
> any major algorithmic differences between FrameSearch and pSM?  Besides
> things like using list files in GCG format?  Are there better ways to do
> what Framesearch does (got pSM from the BP tutorial, but thought maybe
> something in Emboss would work too).

I'm assuming you meant pSW?  If you've got a Canadian collaborator you can
use the Canadian Bioinformatics Resource GeneMatcher and do it in
hardware for free. [plug :-)]

http://www.cbr.nrc.ca/gm/

I think the EMBOSS equivalent of framesearch is wise2, but I don't use
that package much so I may be wrong...

________________________________________________________________________
Paul Gordon                                     Paul.Gordon@nrc.ca
Genomic Technologies				http://maggie.cbr.nrc.ca
Institute for Marine Biosciences
National Research Council Canada