MBE Advance Access originally published online on July 24, 2006
Molecular Biology and Evolution 2006 23(10):1937-1945; doi:10.1093/molbev/msl056
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Research Article |
A Simple Statistical Method for Estimating Type-II (Cluster-Specific) Functional Divergence of Protein Sequences
Department of Genetics, Development and Cell Biology, Center for Bioinformatics and Biological Statistics, Iowa State University
E-mail: xgu{at}iastate.edu.
Predicting functional amino acid residues in silico is important for comparative genomics. In this paper, we focus on the issue of how to statistically identify cluster-specific amino acid residues that are related to the functional divergence after gene duplication. We approach this problem using a framework based on site-specific shift of amino acid property (type-II functional divergence), as opposed to site-specific shift of evolutionary rate (type-I functional divergence). An efficient statistical procedure is implemented to facilitate the development of phylogenomic database for cluster-specific residues of large-scale protein families. Our method has the following features: 1) statistical testing of the type-II functional divergence and 2) the site-specific Bayesian profile to measure how amino acid residues contribute to type-II (cluster-specific) functional divergence. Consequently, one may obtain the posterior probability for "functional" cluster-specific residues. Case studies are presented and indicate that radical cluster-specific residues are responsible for most of inferred type-II functional divergence, whereas conserved cluster-specific residues appear less than even those imperfect radical cluster-specific residues to this type of functional divergence.
Key Words: functional divergence • gene family evolution • cluster-specific sites
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