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 !!).