Profile alignment problems

Steve Thompson: VADMS genetics THOMPSON at WSUVMS1.CSC.WSU.EDU
Tue May 26 17:18:46 EST 1992

Hi GCG'ers:

I sent out the "I'm confused" message regarding problems with Profile
alignments this morning.  Since then I've figured out what was going on and it
was in the GCG documentation all along!!  I've exceeded the "maximum surface of
comparison" parameter for our site.  Therefore, the program was dividing up the
alignment into a series of overlapping sections.  What I failed to notice was
none of the numerous alignments for each sequence was of the same exact area--
they actually "stepped" up along the length of the sequence.  The programs are
working as they are supposed to, albeit, it is not a very efficient manner for
it takes forever and produces huge amounts of data to be perused for anything
meaningful.  Is it possible to alter parameters such that only the "VERY BEST"
area of alignment is retained in the output; after all it is supposed to be a
"LOCAL" alignment algorithm.

					Thanks in advance for any tips,
								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

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