INTRODUCTIONThe original Dayhoff percent accepted mutation (PAM) matrices were developed based on a small number of protein sequences and an evolutionary model of protein change. By extrapolating from the observed changes at small evolutionary distances to large ones, it was possible to establish a PAM250 scoring matrix for sequences that were highly divergent. Another approach to finding a scoring matrix for divergent sequences is to start with a more divergent set of sequences and produce a scoring matrix from the substitutions found in those less-related sequences. The blocks amino acid substitution matrices (BLOSUM) scoring matrices were prepared this way. This article explains how BLOSUM scoring matrices were created and how they can best be used.