Simplified amino acid alphabets based on deviation of conditional probability from random background
Abstract
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.
Cite
@article{arxiv.physics/0211031,
title = {Simplified amino acid alphabets based on deviation of conditional probability from random background},
author = {Xin Liu and Di Liu and Ji Qi and Wei-Mou Zheng},
journal= {arXiv preprint arXiv:physics/0211031},
year = {2009}
}
Comments
9 pages,3figures