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

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

2002-11-07

arxiv.org/abs/physics/0211031v1

PRE 66, 021906 (2002)

Physics

Biological Physics

9 pages,3figures

Scientific paper

10.1103/PhysRevE.66.021906

The primitive data for deducing the Miyazawa-Jernigan contact energy or BLOSUM score matrix consists of pair frequency counts. Each amino acid corresponds to a conditional probability distribution. Based on the deviation of such conditional probability from random background, a scheme for reduction of amino acid alphabet is proposed. It is observed that evident discrepancy exists between reduced alphabets obtained from raw data of the Miyazawa-Jernigan's and BLOSUM's residue pair counts. Taking homologous sequence database SCOP40 as a test set, we detect homology with the obtained coarse-grained substitution matrices. It is verified that the reduced alphabets obtained well preserve information contained in the original 20-letter alphabet.

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