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