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. Author manuscript; available in PMC: 2014 Oct 15.
Published in final edited form as: Curr Protoc Bioinformatics. 2013 Oct 15;43:3.5.1–3.5.9. doi: 10.1002/0471250953.bi0305s43

Figure 1. The BLOSUM62 matrix.

Figure 1

The BLOSUM62 matrix used by BLASTP, BLASTX, and TBLASTN is actually 23 × 23 – 20 amino acids plus ‘X’ (any amino acid), ‘B’ (‘D’ or ‘E’) and ‘Z’ (‘N’ or ‘Q’). Only the lower half of the symmetric matrix is shown to highlight the identity scores on the diagonal. The most positive value is 11 ( ‘W:W’ alignment); the most negative is −4 (found for many hydrophobic/hydrophilic and small/large replacements). The BLOSUM62 matrix is scaled in 1/2-bit units, so the W:W alignment of 11 is 25.5=45 times more common in homologous proteins than by chance. Weighted by amino acid abundance, the average similarity score is about −1 half-bits.