Problems with Profile alignments

Steve Thompson: VADMS genetics THOMPSON at WSUVMS1.CSC.WSU.EDU
Tue May 26 12:26:12 EST 1992


Hello fellow GCG users:

I'm confused.  I've been using the Profile package ever since it first came out
and am very impressed by its power and sensitivity.  (p.s.  I'm setting up an
ftp site here for that list of profiles that I've assembled and many of you
have asked about.  I'll present full details in a posting in the next day or
two.)  However, a problem with ProfileSegments and ProfileGap has recently
surfaced.  In aligning some sequences with some profiles (I haven't been able
to figure out what makes these particular sequences or profiles different other
than they are often quite long) the program goes into various permutations of
the alignment and produces more than one alignment for each of these problem
sequences.  Of these, one is usually clearly better and the others are often
pure garbage.  Obviously this eats up cpu time and creates huge output files. 
Am I doing something wrong?  We are running version 7.1 of GCG under VMS 5.4.

			Thanks in advance for any insight you can provide,
								Steve Thompson

                              Steven M. Thompson
            Consultant in Molecular Genetics and Sequence Analysis
VADMS (Visualization, Analysis & Design in the Molecular Sciences) Laboratory
           Washington State University, Pullman, WA 99164-1224, USA
          AT&Tnet:  (509) 335-0533 or 335-3179  FAX:  (509) 335-0540
                  BITnet:  THOMPSON at WSUVMS1 or STEVET at WSUVM1
                   INTERnet:  THOMPSON at wsuvms1.csc.wsu.edu





More information about the Bio-soft mailing list