Simplified amino acid alphabets based on deviation of conditional probability from random background.


The primitive data for deducing the Miyazawa-Jernigan contact energy or blocks substitution matrix (BLOSUM) consists of pair frequency counts. Each amino acid corresponds to a conditional probability distribution. Based on the deviation of such a conditional probability from random background, a scheme for the reduction of the amino acid alphabet is… (More)
DOI: 10.1103/PhysRevE.66.021906


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