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Protein distance/similarity measure

Nicolas Le Nov=E8re lenov at pasteur.fr
Tue May 19 10:41:52 EST 1998

Brian Foley wrote:

> --      I am in need of a program to calculate pairwise
> similarity scores between amino acid sequences.  I need the
> score to be in the form of % similarity.|

  I wrote a program which computes the conservation per position in
an alignment. In a first step the program computes the global similarity
between every pair of sequences (this value is used afterward to correct
for overrepresention).  You have the choice between several matrices.
Currently they are:


Identity matrix for nucleic acid


Identity matrix for proteins

(you then get an "identity" percentage rather than a similarity one)


The similarity matrix used in the program GAP of the GCG wisconsin
It was modified for my needs (rescaled and gap gestion added).

The default matrix is gcggap.

You can download DOS and UNIX version at:


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