A simple statistical method for estimating type-II (cluster-specific) functional divergence of protein sequences

Molecular Biology and Evolution

Volumn 23, Issue 10, 2006, Pages 1937-1945

  Gu, Xun ^a  

^a IOWA STATE UNIVERSITY   (United States)

Author keywords

Cluster specific sites; Functional divergence; Gene family evolution

Indexed keywords

AMINO ACID;

ARTICLE; BAYES THEOREM; CLUSTER SPECIFIC II FUNCTIONAL DIVERGENCE; COMPARATIVE GENE MAPPING; COMPUTER MODEL; COMPUTER PREDICTION; COMPUTER PROGRAM; CONCEPTUAL FRAMEWORK; GENE; GENETIC VARIABILITY; HAMSTER; HORSE; HUMAN; MOUSE; NONHUMAN; PAX GENE; PROTEIN FAMILY; PROTEIN FUNCTION; PROTEIN STRUCTURE; RABBIT; SEQUENCE ANALYSIS; SHEEP; STATISTICAL ANALYSIS; STRUCTURE ACTIVITY RELATION;

AMINO ACID SEQUENCE; BAYES THEOREM; BIOMETRY; CASPASES; EVOLUTION, MOLECULAR; GENE DUPLICATION; GENOMICS; GTP-BINDING PROTEIN ALPHA SUBUNITS; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; MULTIGENE FAMILY; PHYLOGENY; PROSTAGLANDIN-ENDOPEROXIDE SYNTHASES; PROTEINS; SEQUENCE ALIGNMENT;

EID: 33748784344     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msl056     Document Type: Article

References (33)

1. Atchley WR, Zhao J, Fernandes A, Drueke T. 2005. Solving the sequence 'metric' problem. Proc Natl Acad Sci 102: 6395-400.
2. Dayhoff MO, Schwartz RM, Orcutt BC. 1978. A model of evolutionary change in proteins. In: Dayhoff MO, editor. Atlas of protein sequence structure. Volume 5. Suppl 3. Washington, DC: National Biomedical Research Foundation. p 342-52.
3. Eisen MB, Fraser CM. 2003. Phylogenomics: intersection of evolution and genomics. Science 300:1706-7.
4. Felsenstein J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368-76.
5. Force A, Lynch M, Pickett FB, Amores A, Yan YL, Postlethwait J. 1999. Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151:1531-45.
6. Gao X, Vander Velden K, Voytas DF, Gu X. 2005. SplitTester: software to identify domains responsible for functional divergence in protein family. BMC Bioinformatics 6:137.
7. Gaucher EA, Gu X, Miyamoto M, Benner S. 2002. Predicting functional divergence in protein evolution by site-specific rate shifts. Trend Biochem Sci 27:315-21.
8. Golding GB, Dean AM. 1998. The structural basis of molecular adaptation. Mol Biol Evol 15:355-69.
9. Gribaldo S, Casane D, Lopez P, Philippea H. 2003. Functional divergence prediction from evolutionary analysis: a case study of vertebrate hemoglobin. Mol Biol Evol 20:1754-9.
10. Gu X. 1999. Statistical methods for testing functional divergence after gene duplication. Mol Biol Evol 16:1664-74.
11. Gu X. 2001. Maximum likelihood approach for gene family evolution under functional divergence. Mol Biol Evol 18:453-64.
12. Gu X. 2003. Functional divergence in protein (family) sequence evolution. Genetica 118:133-41.
13. Gu X, Fu YX, Li WH. 1995. Maximum likelihood estimation of the heterogeneity of substitution rate among nucleotide sites. Mol Biol Evol 12:546-57.
14. Gu X, Li WH. 1995. The size distribution of insertions and deletions in human and rodent pseudogenes suggests the logarithmic gap penalty for sequence alignment. J Mol Evol 40: 464-73.
15. Gu X, Vander Velden K. 2002. DIVERGE: phylogeny-based analysis for functional-structural divergence of a protein family. Bioinformatics 18:500-1.
16. Gu X, Zhang J. 1997. A simple method for estimating the parameter of substitution rate variation among sites. Mol Biol Evol 14:1106-13.
17. Jones DT, Taylor WR, Thornton JM. 1992. The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci 8:275-82.
18. Jordan K, Bishop GR, Gonzalez DS. 2001. Sequence and structural aspects of functional diversification in class I α-mannosidase evolution. Bioinformatics 17:965-76.
19. Kimura M. 1983. The neutral theory of molecular evolution. Cambridge: Cambridge University Press.
20. Knudsen B, Miyamoto MM. 2001. A likelihood ratio test for evolutionary rate shifts and functional divergence among proteins. Proc Natl Acad Sci 98:14512-7.
21. Landgraf R, Xenarios I, Eisenberg D. 2001. Three-dimensional cluster analysis identifies interfaces and functional residue clusters in proteins. J Mol Biol 307:1487-502.
22. Li X, Hu C, Liang J. 2003. Simplicial edge representation of protein structures and alpha contact potential with confidence measure. Proteins 53:792-805.
23. Lichtarge O, Bourne HR, Cohen FE. 1996. An evolutionary trace method defines binding surfaces common to protein families. J Mol Biol 257:342-58.
24. Lopez P, Forterre P, Philippe H. 1999. The root of the tree of life in the light of the covarion model. J Mol Evol 49: 496-508.
25. Madabushi S, Gross AK, Philippi A, Meng EC, Wensel TG, Lichtarge O. 2004. Evolutionary trace of G protein-coupled receptors reveals clusters of residues that determine global and class-specific functions. J Biol Chem 279:8126-32.
26. Murphy L, Wallqvist A, Levy R. 2000. Simplified amino acid alphabets for protein fold recognition and implications for folding. Protein 13:149-52.
27. Ohno S. 1970. Evolution by gene duplication. Berlin: Springer-Verlag.
28. Rastogi S, Liberles D. 2005. Subfunctionalization of duplicated genes as a transition state to neofunctionalization. BMC Evol Biol 5:28.
29. Sun H, Merugu S, Gu X, Kang Y, Dickinson DP, Callaerts P, Li W-H. 2002. Identification of essential amino acid changes in paired domain evolution using a novel combination of evolutionary analysis and in vitro and in vivo studies. Mol Biol Evol 19:1490-500.
30. Tseng YY, Liang J. 2006. Estimation of amino acid residue substitution rates at local spatial regions and application in protein function inference: a Bayesian Monte Carlo approach. Mol Biol Evol 23:421-36.
31. Wang Y, Gu X. 2001. Predicting functional divergence of caspase gene family. Genetics 158:1311-20.
32. Yang Z, Kumar S, Nei M. 1995. A new method of inference of ancestral nucleotide and amino acid sequences. Genetics 141:1641-50.
33. Zhang J, Nei M. 1997. Accuracies of ancestral amino acid sequence inferred by the parsimony, likelihood, and distance method. J Mol Evol 44:S139-46.