> > I'm looking for a non-commercial software for UNIX or Mac (also a
> > web server) that:
> > 1) uses a multiple sequence alignment in GCG form as input.
> > 2) output the degree of sequence conservation in the multialignment
> > in order to find (and define) in an objective way the limits of similar
> > sequence regions.
> > In fact, I'm looking for a UNIX or Mac soft similar to the
> > described by Friemann & Schmitz in "A new approach for displaying
> > identities and differences among aligned amino acid sequences. (1992).
> > CABIOS 8(3):261-165."
Years ago I wrote a very crude program, ConsIndex, which output
a position-specific index according to the substitution matrix
choosen. You can find it at:
And see an example of use in:
Le Novère N, Corringer, PJ and Changeux JP (1999). Improved
secondary structure predictions for a nicotinic receptor subunit.
Incorporation of solvent accessibility and experimental data into
a 2D representation. Biophys J 76 : 2329-2345
Nicolas Le Novère
Neurobiologie Moléculaire, Institut Pasteur, 75724 Paris cedex FR
e-mail : lenov at pasteur.fr, http://www.pasteur.fr/units/neubiomol/
tel : 33-(01)-45-68-88-44 fax : 33-(01)-45-68-88-36