RE- weight matrix

Brett Lindenbach Brett_Lindenbach at QMS1.LIFE.UIUC.EDU
Tue Jun 9 18:37:56 EST 1992

                       Subject:                               Time:5:23
  OFFICE MEMO          RE: weight matrix                     
Mark Berres asks:
>Does any one know the particular weighting matrix used by the Gap
>program in the GCG package?  I am having difficulty reproducing some 
>published alignments based on that program utilizing alternative
>alignment progs such as Genalign, Clustalv etc. which allow for
>PAM 250, 100 and Identity matrices.  If indeed another form of        
        >weighting matrix is used in GCG Gap, is there a published
>in which a description and justification exists?

Mark, the GAP program in the GCG package uses the standard Needleman &
Wunsch method, with amino acid substititions allowed by the Dayhoff
measurement, as normalized by Gribskov (Gribskov and Burgess (1986)
Nucl. Acid Res. 14(16) 6745-6763). It also accepts alternate weight
tables and user input gap/gap-length weight. 

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