A substitution matrix is a matrix used in bioinformatics (and also in computational biology) to determine/estimate the rate at which one character -which is specified by a nucleotide sequence in nucleic acid alignments or by one amino acid in protein alignments-, changed to another character during the course of the evolution. The BLOcks SUbstitution Matrix (popularly known as BLOSUM) is a substitution matrix used to score one amino acid for another in a protein alignment. The BLOSUM substitution matrix is particularly useful to compare evolutionarily conserved regions between protein sequences and thus score their alignments, where each entry is indicated by a similarity score between two amino acids.
