DOI: 10.1093/molbev/msl056. A Simple Statistical Method for Estimating Type-II (Cluster-Specific) Functional Divergence of Protein Sequences

A Simple Statistical Method for Estimating Type-II (Cluster-Specific) Functional Divergence of Protein Sequences

10.1093/molbev/msl056

Crossref journal-article

Oxford University Press (OUP)

Molecular Biology and Evolution (286)

Bibliography

Gu, X. (2006). A Simple Statistical Method for Estimating Type-II (Cluster-Specific) Functional Divergence of Protein Sequences. Molecular Biology and Evolution, 23(10), 1937â1945.

Authors 1

Xun Gu (first)

References 33 Referenced 170

Atchley WR, Zhao J, Fernandes A, Drueke T. 2005. Solving the sequence ‘metric’ problem. Proc Natl Acad Sci102:6395–400. (10.1073/pnas.0408677102)
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.
Eisen MB, Fraser CM. 2003. Phylogenomics: intersection of evolution and genomics. Science300:1706–7. (10.1126/science.1086292)
Felsenstein J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol17:368–76. (10.1007/BF01734359)
Force A, Lynch M, Pickett FB, Amores A, Yan YL, Postlethwait J. 1999. Preservation of duplicate genes by complementary, degenerative mutations. Genetics151:1531–45. (10.1093/genetics/151.4.1531)
Gao X, Vander Velden K, Voytas DF, Gu X. 2005. SplitTester: software to identify domains responsible for functional divergence in protein family. BMC Bioinformatics6:137. (10.1186/1471-2105-6-137)
Gaucher EA, Gu X, Miyamoto M, Benner S. 2002. Predicting functional divergence in protein evolution by site-specific rate shifts. Trend Biochem Sci27:315–21. (10.1016/S0968-0004(02)02094-7)
Golding GB, Dean AM. 1998. The structural basis of molecular adaptation. Mol Biol Evol15:355–69. (10.1093/oxfordjournals.molbev.a025932)
Gribaldo S, Casane D, Lopez P, Philippea H. 2003. Functional divergence prediction from evolutionary analysis: a case study of vertebrate hemoglobin. Mol Biol Evol20:1754–9. (10.1093/molbev/msg171)
Gu X. 1999. Statistical methods for testing functional divergence after gene duplication. Mol Biol Evol16:1664–74. (10.1093/oxfordjournals.molbev.a026080)
Gu X. 2001. Maximum likelihood approach for gene family evolution under functional divergence. Mol Biol Evol18:453–64. (10.1093/oxfordjournals.molbev.a003824)
Gu X. 2003. Functional divergence in protein (family) sequence evolution. Genetica118:133–41. (10.1023/A:1024197424306)
Gu X, Fu YX, Li WH. 1995. Maximum likelihood estimation of the heterogeneity of substitution rate among nucleotide sites. Mol Biol Evol12:546–57.
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 Evol40:464–73. (10.1007/BF00164032)
Gu X, Vander Velden K. 2002. DIVERGE: phylogeny-based analysis for functional-structural divergence of a protein family. Bioinformatics18:500–1. (10.1093/bioinformatics/18.3.500)
Gu X, Zhang J. 1997. A simple method for estimating the parameter of substitution rate variation among sites. Mol Biol Evol14:1106–13. (10.1093/oxfordjournals.molbev.a025720)
Jones DT, Taylor WR, Thornton JM. 1992. The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci8:275–82. (10.1093/bioinformatics/8.3.275)
Jordan K, Bishop GR, Gonzalez DS. 2001. Sequence and structural aspects of functional diversification in class I α-mannosidase evolution. Bioinformatics17:965–76. (10.1093/bioinformatics/17.10.965)
Kimura M. 1983. The neutral theory of molecular evolution. Cambridge: Cambridge University Press. (10.1017/CBO9780511623486)
Knudsen B, Miyamoto MM. 2001. A likelihood ratio test for evolutionary rate shifts and functional divergence among proteins. Proc Natl Acad Sci98:14512–7. (10.1073/pnas.251526398)
Landgraf R, Xenarios I, Eisenberg D. 2001. Three-dimensional cluster analysis identifies interfaces and functional residue clusters in proteins. J Mol Biol307:1487–502. (10.1006/jmbi.2001.4540)
Li X, Hu C, Liang J. 2003. Simplicial edge representation of protein structures and alpha contact potential with confidence measure. Proteins53:792–805. (10.1002/prot.10442)
Lichtarge O, Bourne HR, Cohen FE. 1996. An evolutionary trace method defines binding surfaces common to protein families. J Mol Biol257:342–58. (10.1006/jmbi.1996.0167)
Lopez P, Forterre P, Philippe H. 1999. The root of the tree of life in the light of the covarion model. J Mol Evol49:496–508. (10.1007/PL00006572)
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 Chem279:8126–32. (10.1074/jbc.M312671200)
Murphy L, Wallqvist A, Levy R. 2000. Simplified amino acid alphabets for protein fold recognition and implications for folding. Protein13:149–52. (10.1093/protein/13.3.149)
Ohno S. 1970. Evolution by gene duplication. Berlin: Springer-Verlag. (10.1007/978-3-642-86659-3)
Rastogi S, Liberles D. 2005. Subfunctionalization of duplicated genes as a transition state to neofunctionalization. BMC Evol Biol5:28. (10.1186/1471-2148-5-28)
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 Evol19:1490–500. (10.1093/oxfordjournals.molbev.a004212)
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 Evol23:421–36. (10.1093/molbev/msj048)
Wang Y, Gu X. 2001. Predicting functional divergence of caspase gene family. Genetics158:1311–20. (10.1093/genetics/158.3.1311)
Yang Z, Kumar S, Nei M. 1995. A new method of inference of ancestral nucleotide and amino acid sequences. Genetics141:1641–50. (10.1093/genetics/141.4.1641)
Zhang J, Nei M. 1997. Accuracies of ancestral amino acid sequence inferred by the parsimony, likelihood, and distance method. J Mol Evol44:S139–46. (10.1007/PL00000067)

Dates

Type	When
Created	19 years, 1 month ago (July 24, 2006, 8:13 p.m.)
Deposited	4 years, 1 month ago (July 30, 2021, 2:02 a.m.)
Indexed	3 days, 23 hours ago (Sept. 3, 2025, 5:50 a.m.)
Issued	19 years, 1 month ago (July 24, 2006)
Published	19 years, 1 month ago (July 24, 2006)
Published Online	19 years, 1 month ago (July 24, 2006)
Published Print	18 years, 11 months ago (Oct. 1, 2006)

Funders 0

None

BibTeX

@article{Gu_2006, title={A Simple Statistical Method for Estimating Type-II (Cluster-Specific) Functional Divergence of Protein Sequences}, volume={23}, ISSN={0737-4038}, url={http://dx.doi.org/10.1093/molbev/msl056}, DOI={10.1093/molbev/msl056}, number={10}, journal={Molecular Biology and Evolution}, publisher={Oxford University Press (OUP)}, author={Gu, Xun}, year={2006}, month=jul, pages={1937–1945} }

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