BLOSUM

BLOSUM (BLOcks of Amino Acid SUbstitution Matrix) is a substitution matrix used for sequence alignment of proteins. BLOSUM matrices are used to score alignments between evolutionarily divergent protein sequences. Blosum is based on local alignments. Blosum was first introduced in a paper by Henikoff and Henikoff (1992; PNAS 89:10915-10919). They scanned the BLOCKS database for very conserved regions of protein families (that do not have gaps in the sequence alignment) and then counted the relative frequencies of amino acids and their substitution probabilities. Then, they calculated a log-odds score for each of the 210 possible substitutions of the 20 standard amino acids. All Blosum matrices are based on observed alignments; they are not extrapolated from comparisons or closely related proteins.

Blosum matrices with high numbers are designed for comparing closely related sequences, while Blosum matrices with low numbers are designed for comparing distant related sequences. For example, Blosum80 is used for less divergent alignments, and Blosum45 is used for more divergent alignments. Scores within a Blosum matix are log-odds scores that measure the logarithm for the ratio of the likelihood of two amino acids appearing by chance.  The matrices are based on the minimum percentage identity of the aligned protein sequence used in calculating them.  Every possible identity or substitution is assigned a score based on its observed frequences in the alignment of related proteins.  A positive score is given to the more likely substitutions while a negative score is given to the less likely substitutions.

BLOSUM62 is the matrix calculated by using the observed substitutions between proteins which have 62% or more sequence identity. BLOSUM has proved better at scoring distantly related sequences than the once-widely-used Point Accepted Mutation (PAM) matrices. To calculate a matrix for Blosum62, the following equation is used: B[i,j]= (1/λ)log {(P i,j)/(ƒi,ƒj)}