GCG V. 9.0-GAP
cgovaert at ulb.ac.be
Tue May 27 04:19:46 EST 1997
In article <5mdbsh$ec0 at netnews.upenn.edu>, ellis at vesicle.dental.upenn.edu
>As indicated below, the scoring matricies are indeed the problem. A simple
solution is to add the
>following to your gap commands: -matr=oldpep.cmp. This uses the version 8
matrix, and gives the
>same fits as version 8.
But the renormalized matrix used by GCG 8 has no scientific value, because
a conserved Glycine is in fact different than a conserved Tryptophan..
Better use Blosum 62 or PAM 250 (not renormalized !!).
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