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
