GCG V. 9.0-GAP

[Cedric Govaerts]

In article <5mdbsh$ec0 at netnews.upenn.edu>, ellis at vesicle.dental.upenn.edu 
says...
>
>
>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.  
>
>Ellis Golub
>


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 !!).

Cedric Govaerts