;BLOSUM: Blocks Substitution Matrix, a substitution matrix used for sequence alignment of proteins.
;Scoring metrics (statistical versus biological): When evaluating a sequence alignment, one would like to know how meaningful it is. This requires a scoring matrix, or a table of values that describes the probability of a biologically meaningful amino-acid or nucleotide residue-pair occurring in an alignment. Scores for each position are obtained frequencies of substitutions in blocks of local alignments of protein sequences.
;BLOSUM r:
:The matrix built from blocks with less than r% of similarity
:* E.g., BLOSUM62 is the matrix built using sequences with less than 62% similarity (sequences with ≥ 62% identity were clustered)
:* Note: BLOSUM 62 is the default matrix for protein BLAST. Experimentation has shown that the BLOSUM-62 matrix is among the best for detecting most weak protein similarities.
Several sets of BLOSUM matrices exist using different alignment databases, named with numbers. BLOSUM matrices with high numbers are designed for comparing closely related sequences, while those with low numbers are designed for comparing distant related sequences. For example, BLOSUM80 is used for closely related alignments, and BLOSUM45 is used for more distantly related alignments. The matrices were created by merging (clustering) all sequences that were more similar than a given percentage into one single sequence and then comparing those sequences (that were all more divergent than the given percentage value) only; thus reducing the contribution of closely related sequences. The percentage used was appended to the name, giving BLOSUM80 for example where sequences that were more than 80% identical were clustered.