The BLOSUM62 matrix quantifies the similarity of amino acids to one another when computing evolutionary distance sequences (1). Interestingly, it has math errors in its computation that make it a more effective matrix for substitution calculation (2). A custom version for TCRs has also been presented (3).
1.
Henikoff S, Henikoff JG. Amino acid substitution matrices from protein blocks. Proceedings of the National Academy of Sciences. 1992;89(22):10915–9. Available from: https://doi.org/10.1073/pnas.89.22.10915
2.
Styczynski MP, Jensen KL, Rigoutsos I, Stephanopoulos G. BLOSUM62 miscalculations improve search performance. Nature Biotechnology. 2008;26(3):274–5. Available from: https://doi.org/10.1038/nbt0308-274
3.
Postovskaya A, Vercauteren K, Meysman P, Laukens K. tcrBLOSUM: an amino acid substitution matrix for sensitive alignment of distant epitope-specific TCRs. Briefings in Bioinformatics. 2024;26(1). Available from: https://doi.org/10.1093/bib/bbae602