[Bioperl-l] pSM vs .Framesearch

Wiepert, Mathieu Wiepert.Mathieu@mayo.edu
Thu, 23 Aug 2001 07:48:13 -0500


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).