Amino acid substitution matrices.

The BLOSUM (BLOck SUbstitution Matrices) matrices were derived by Steven and Jorja Henikoff in 1992 1. They were based on a much larger data set than the PAM matrices, and used conserved local alignments or “blocks,” rather than global alignments of very closely related sequences. In order to account for different degrees of sequence divergence, the Henikoffs used clustering rather than an explicit evolutionary model. Clustering with different values of n, ranging from 45% to 90%, produces a parameterized set of matrices representing different degrees of sequence divergence. The clustering procedure also addressed the issue of sample bias.