Computing degrees of sequence conservation in multialignedsequences

Nicolas Le Novère lenov at pasteur.fr
Wed Jul 26 09:33:21 EST 2000

> >         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

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