In article <1993Mar3.225233.19116 at newssun.med.miami.edu>, sdorazio at miasun.med.miami.edu (Sarah Dorazio) writes:
>I have been using the GCG Gap and Bestfit programs to make
>amino acid sequence comparisons between related proteins. I
>recently learned that implementing something called
>the"Dayhoff matrix" would be better for this purpose.
The GCG Gap and Bestfit programs use the Dayhoff scoring matrix to
determine the score of a match. The exact matrix used by GAP and
Bestfit are slightly different from the original Dayhoff scoring
matrix -- they have been rescaled and normalized. See the comments in
the GCG comparison table files called:
GENRUNDATA:SWGAPPEP.CMP for GAP
GENRUNDATA:NWSGAPPEP.CMP for BESTFIT
(The tables and transformation from Dayhoff are the same between these
two tables. But GAP uses one and BESTFIT the other.)
Another scoring matrix was published last year in Science (1992)
256:1443-1445 by Gonnet et al and is available in GCG format, TEXT
file and as a Macintosh Excel table via Anonymous ftp from
amber.mgh.harvard.edu in the directory gonnet.
Mike
