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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]

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]

Researcher in bioinformatics who, with Steven Henikoff, developed amino acid substitution matrices from conserved protein blocks. These matrices turn observed replacement patterns into scores for protein sequence alignment.^[ref]

A multiple sequence alignment places three or more sequences in corresponding columns, inserting gaps where needed. The arrangement represents a hypothesis about positional correspondence and can support phylogenetics or detection of conserved motifs. A column can be reliably aligned in one region and ambiguous in another. Adding sequences can clarify shared structure but also introduce difficult divergent regions, so the alignment itself requires evaluation before downstream inference. ^[ref]

A diagonal substitution matrix score measures enrichment over a background match, rather than simply rewarding an identical letter. tryptophan residues are comparatively rare, so a W–W match has a small chance background frequency $p_W^2$. Its observed conservation produces a much larger ratio $q_{WW}/p_W^2$ than the corresponding ratio for the more common leucine. The BLOSUM62 diagonal therefore awards W–W more than L–L. Both the background frequency and the observed pair frequency matter; rarity alone does not determine a diagonal score.^[ref]

The number specifies the sequence-identity threshold used when clustering related sequences before deriving a BLOSUM substitution matrix. At 62%, sufficiently similar sequences are grouped and their within-cluster comparisons are excluded. Lowering the threshold merges more sequences, emphasizing comparisons across greater divergence.

Consequently BLOSUM80 is suited to closer relatives, BLOSUM45 to more divergent sequences, and BLOSUM62 is intermediate. The numbers do not specify a required identity of the query and target, nor a number of evolutionary time steps.^[ref]

Researcher in chromatin biology and bioinformatics. With Jorja G. Henikoff, Henikoff developed amino acid substitution matrices from conserved protein blocks; these provide empirically grounded scores for comparing protein sequences.^[ref]