Subject: Time:5:23
PM
OFFICE MEMO RE: weight matrix
Date:6/9/92
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
reference
>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.
