Hi experts,

We have the following problem in scoring multiple aligned proteins and
 generating a similarity matrix.

For i = 1,2,...,20 amino acids, a substition of amino acid i -> j results in a
 similarity s_ij. Note that s_ii >> 0 for most amino acids (i.e., amino acid i
 has similarity to itself of s_ii >> 0).

We can generate a similarity 'score' matrix for a set of N proteins but the
 diagonals >> 1. We would like to scale this matrix so each diagonal is 1, and
 each off-diagonal element is 0 <= s_ij <= 1.

Thanks for any suggestions.
Bill

PS -- for protein alignment experts we are using the BLOSUM62 score matrix and
 working with already multiple aligned proteins.

--

William D. Shannon, Ph.D.

Assistant Professor of Biostatistics in Medicine
Division of General Medical Sciences and Biostatistics

Washington University School of Medicine
Campus Box 8005, 660 S. Euclid
St. Louis, MO   63110

Phone: 314-454-8356
Fax: 314-454-5113
e-mail: [log in to unmask]
web page: http://ilya.wustl.edu/~shannon