A unified statistical model of protein multiple sequence alignment integrating direct coupling and insertions.

ABSTRACT: The multiple sequence alignment (MSA) of a protein family provides a wealth of information in terms of the conservation pattern of amino acid residues not only at each alignment site but also between distant sites. In order to statistically model the MSA incorporating both short-range and long-range correlations as well as insertions, I have derived a lattice gas model of the MSA based on the principle of maximum entropy. The partition function, obtained by the transfer matrix method with a mean-field approximation, accounts for all possible alignments with all possible sequences. The model parameters for short-range and long-range interactions were determined by a self-consistent condition and by a Gaussian approximation, respectively. Using this model with and without long-range interact

SUBMITTER: Kinjo AR 

PROVIDER: S-EPMC5042171 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature