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
BLOSUM, short for "Blocks Substitution Matrix," refers to a series of substitution matrices used for sequence alignment, primarily in the field of bioinformatics. These matrices are designed to score alignments between protein sequences based on observed substitutions in blocks of homologous sequences. The BLOSUM matrices are indexed by a number (BLOSUM62, BLOSUM80, etc.), where the number indicates the minimum level of sequence identity among the sequences used to create the matrix.
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