A substitution matrix assigns a score to aligning each pair of sequence symbols. Scores based on logarithms of observed-to-background pair frequencies turn products of relative support into additive alignment scores.
A BLOSUM matrix assigns amino-acid substitution scores estimated from conserved aligned blocks of proteins. Related sequences are clustered to reduce overrepresentation, and observed replacement frequencies are compared with background frequencies. Positive scores favour a pairing relative to that background; negative scores disfavor it. The matrix number identifies the clustering identity threshold, not the percentage identity of every sequence pair to which the matrix can be applied. [ref]
Amino acid substitution matrices from protein blocks by Steven Henikoff and Jorja G. Henikoff. 1992, block construction, clustering and log-odds scores
BLOSUM62 is a BLOSUM amino-acid substitution matrix constructed using a 62-percent sequence-identity clustering threshold for the contributing blocks. It is widely used in protein sequence alignment. Its substitution scores form only one part of a complete alignment scheme: gap costs and local versus global objectives also affect the result. The number 62 describes construction of the matrix rather than a required identity of the query and target. [ref]
Amino acid substitution matrices from protein blocks by Steven Henikoff and Jorja G. Henikoff. 1992, BLOSUM family and clustering thresholds
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A substitution matrix is a mathematical tool used primarily in bioinformatics to score alignments of biological sequences, such as DNA, RNA, or protein sequences. It quantifies the likelihood of one character (nucleotide or amino acid) being replaced by another during the evolution of organisms.