Pairwise protein align. program wanted

Francois Jeanmougin pingouin at .u-strasbg.fr
Thu Jun 6 05:11:52 EST 1996

In article <Pine.SOL.3.93.960603005240.2951A-100000 at evolution>,
	Morten Stig Andersen <moan at evolution.bmc.uu.se> writes:
>I am looking for a freeware pairwise alignment program (for unix) which
>can report percent similarity as well as percent identity, like the
>'bestfit' and 'gap' programs in GCG. 
>I have Bill Pearson's 'align' program, but it reports identity only.
>Any clues?
>Morten Andersen
Please, stop talking about percent similarity. There is no information in 
percent similarity. If you want to talk about percent similarity, you have
to cite the matrix you use, and noone is able to say what scores are in a
matrix...In a protein, you can easily see that similarity depends of the
position in the sequence. You can not define the same similarity (in terms of
functional analysis) for a reisdue in an helix, a loop, a sheet or in the
active site.
	Well, I'm not in the better place to give such lessons, but noone else
want to do that...

Francois Jeanmougin
Service de bioinformatique / bioinformatic service
BP 163 
67404 Illkirch France
tel : (33) 88 65 32 71
e-mail : jeanmougin at igbmc.u-strasbg.fr

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