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- Title
Where did the BLOSUM62 alignment score matrix come from?
- Authors
Eddy, Sean R.
- Abstract
The article makes observations concerning the origin and use of BLOSUM62 amino acid score matrix in sequence alignment programs. It uses the method of log-odd scores to know whether two sequences are homologous. The article observes that the definition of "conservative substitution," in a score matrix is purely statistical and has nothing to do with the amino acid structure. In the homologous alignment data that BLOSUM62 was trained on, lucine/leucine (L/L) pairs were in fact more common than tryptophan/tryptophan (W/W) pairs but tryptophan is a much rarer amino acid and one gets +3.8 for L/L and +10.5 for W/W.
- Subjects
AMINO acids; MATRICES (Mathematics); IMINO compounds; TRYPTOPHAN; LOGARITHMS; LOGARITHMIC functions
- Publication
Nature Biotechnology, 2004, Vol 22, Issue 8, p1035
- ISSN
1087-0156
- Publication type
Article
- DOI
10.1038/nbt0804-1035