%I #9 Jul 13 2020 06:22:36

%S 9,-1,4,-1,1,5,-3,-1,-1,7,0,1,0,-1,4,-3,0,-2,-2,0,6,-3,1,0,-2,-2,0,6,

%T -3,0,-1,-1,-2,-1,1,6,-4,0,-1,-1,-1,-2,0,2,5,-3,0,-1,-1,-1,-2,0,0,2,5,

%U -3,-1,-2,-2,-2,-2,1,-1,0,0,8,-3,-1,-1,-2,-1,-2,0,-2,0,1,0,5,-3,0,-1,-1,-1,-2,0,-1,1,1,-1,2,5,-1,-1,-1,-2,-1,-3,-2,-3,-2,0,-2,-1,-1,5,-1,-2,-1,-3,-1,-4,-3,-3,-3,-3,-3,-3,-3,1,4,-1,-2,-1,-3,-1,-4,-3,-4,-3,-2,-3,-2,-2,2,2,4,-1,-2,0,-2,0,-3,-3,-3,-2,-2,-3,-3,-2,1,3,1,4,-2,-2,-2,-4,-2,-3,-3,-3,-3,-3,-1,-3,-3,0,0,0,-1,6,-2,-2,-2,-3,-2,-3,-2,-3,-2,-1,2,-2,-2,-1,-1,-1,-1,3,7,-2,-3,-2,-4,-3,-2,-4,-4,-3,-2,-2,-3,-3,-1,-3,-2,-3,1,2,11

%N BLOSUM62 substitution scoring matrix used to score alignments between evolutionarily divergent protein sequences.

%C The BLOSUM62 (BLocks SUbstitution Matrix) was introduced by Steven and Jorja Henikoff by scanning the BLOCKS database for very conserved regions of protein families (that do not have gaps in the sequence alignment) using sequences with >= 62% identity.

%C The sequences were then clustered and relative frequencies of amino acids and their substitution probabilities were calculated.

%C Then, they calculated a log-odds score for each of the 210 possible substitution pairs of the 20 standard amino acids.

%C The BLOSUM-62 matrix is among the best for detecting most weak protein similarities and still remains the default substitution matrix used by the software BLAST (Basic Local Alignment Search Tool) by the NCBI (National Center for Biotechnology Information).

%C The original authors made a miscalculation in their algorithms that generated the matrix, though surprisingly the miscalculated BLOSUM62 matrix has a better search performance than the corrected version.

%H S. Henikoff and J. G. Henikoff, <a href="https://doi.org/10.1073/pnas.89.22.10915">Amino Acid Substitution Matrices from Protein Blocks</a>, PNAS, (1992), 89 (22): 10915-10919.

%e The substitution matrix can be written as follows for each of the 20 amino acids using their single letter codes arranged by biochemical properties.

%e A positive score is given to the more likely substitutions while a negative score is given to the less likely substitutions.

%e C 9

%e S -1 4

%e T -1 1 5

%e P -3 -1 -1 7

%e A 0 1 0 -1 4

%e G -3 0 -2 -2 0 6

%e N -3 1 0 -2 -2 0 6

%e D -3 0 -1 -1 -2 -1 1 6

%e E -4 0 -1 -1 -1 -2 0 2 5

%e Q -3 0 -1 -1 -1 -2 0 0 2 5

%e H -3 -1 -2 -2 -2 -2 1 -1 0 0 8

%e R -3 -1 -1 -2 -1 -2 0 -2 0 1 0 5

%e K -3 0 -1 -1 -1 -2 0 -1 1 1 -1 2 5

%e M -1 -1 -1 -2 -1 -3 -2 -3 -2 0 -2 -1 -1 5

%e I -1 -2 -1 -3 -1 -4 -3 -3 -3 -3 -3 -3 -3 1 4

%e L -1 -2 -1 -3 -1 -4 -3 -4 -3 -2 -3 -2 -2 2 2 4

%e V -1 -2 0 -2 0 -3 -3 -3 -2 -2 -3 -3 -2 1 3 1 4

%e F -2 -2 -2 -4 -2 -3 -3 -3 -3 -3 -1 -3 -3 0 0 0 -1 6

%e Y -2 -2 -2 -3 -2 -3 -2 -3 -2 -1 2 -2 -2 -1 -1 -1 -1 3 7

%e W -2 -3 -2 -4 -3 -2 -4 -4 -3 -2 -2 -3 -3 -1 -3 -2 -3 1 2 11

%e C S T P A G N D E Q H R K M I L V F Y W

%K sign,fini,full

%O 1,1

%A _T. Jeffrey Cole_, Jun 12 2020