GCG MSF weight fields

Steve Thompson: VADMS genetics THOMPSON at WSUVMS1.CSC.WSU.EDU
Wed Jun 23 11:26:06 EST 1993

Hello Keith and fellow Info-GCG'ers -

In Message-Id: <9306231243.AA09730 at net.bio.net> robison1 at husc10.harvard.edu
(Keith Robison) asked:
>Do any of the GCG programs use the Weight field in the MSF files?
>(in particular PileUp).  Is this just for future expansion?
The weight fields are an often ignored yet extremely powerful feature of MSF
files.  A few of GCG's multiple sequence analysis programs can utilize them;
however, PileUp, when fed a MSF file as input, will not.  They are especially
important when building Profiles and/or consensus sequences from MSF files. 
One does NOT want to bias the results of these types of analyses by over or
under-representing particular sequences.  See the program documentation on both
Prettty and ProfileMake for further explanation.  If you have Rick Westerman's
PrettyBox installed, it also does utilize the weight feature and can often be
used to drastically improve the appearance of the resulting graphic.

						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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