An update of DIVERGE software for functional divergence analysis of protein family

Molecular Biology and Evolution

Volumn 30, Issue 7, 2013, Pages 1713-1719

  Gu, Xun ^a,b   Zou, Yangyun ^a   Su, Zhixi ^a   Huang, Wei ^a   Zhou, Zhan ^a   Arendsee, Zebulun ^b   Zeng, Yanwu ^c  

^a FUDAN UNIVERSITY   (China)

^b IOWA STATE UNIVERSITY   (United States)

^c SHANGHAI JIAO TONG UNIVERSITY SCHOOL OF MEDICINE   (China)

Author keywords

DIVERGE; gene duplication; gene family evolution; type I functional divergence; type II functional divergence

Indexed keywords

AMINO ACID;

AMINO ACID SEQUENCE; ARTICLE; BINDING SITE; COMPUTER PROGRAM; EVOLUTION; GENE CLUSTER; GENE DUPLICATION; PHYLOGENY; PROTEIN ANALYSIS; PROTEIN FUNCTION; RELIABILITY;

DIVERGE; GENE DUPLICATION; GENE FAMILY EVOLUTION; TYPE I FUNCTIONAL DIVERGENCE; TYPE II FUNCTIONAL DIVERGENCE;

AMINO ACID SEQUENCE; AMINO ACIDS; ANIMALS; EVOLUTION, MOLECULAR; GENE DUPLICATION; INDEL MUTATION; MODELS, GENETIC; MULTIGENE FAMILY; PHYLOGENY; PROTEINS; SOFTWARE; VERTEBRATES;

EID: 84878925597     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/mst069     Document Type: Article

References (58)

1. Abhiman S, Sonnhammer EL. 2005a. FunShift: a database of function shift analysis on protein subfamilies. Nucleic Acids Res. 33:D197-D200. (Pubitemid 40207859)
2. Abhiman S, Sonnhammer EL. 2005b. Large-scale prediction of function shift in protein families with a focus on enzymatic function. Proteins 60:758-768. (Pubitemid 41266433)
3. Arnau V, Gallach M, Lucas JI, Marin I. 2006. UVPAR: fast detection of functional shifts in duplicate genes. BMC Bioinformatics 7:174.
4. Benitez-Paez A, Cardenas-Brito S, Gutierrez AJ. 2012. A practical guide for the computational selection of residues to be experimentally characterized in protein families. Brief Bioinform. 13:329-336.
5. Bharatham K, Zhang ZH, Mihalek I. 2011. Determinants, discriminants, conserved residues-a heuristic approach to detection of functional divergence in protein families. PLoS One 6:e24382.
6. Blouin C, Boucher Y, Roger AJ. 2003. Inferring functional constraints and divergence in protein families using 3D mapping of phylogenetic information. Nucleic Acids Res. 31:790-797. (Pubitemid 36175969)
7. Brandt BW, Feenstra KA, Heringa J. 2010. Multi-harmony: detecting functional specificity from sequence alignment. Nucleic Acids Res. 38:W35-W40.
8. Capra JA, SinghM. 2008. Characterization and prediction of residues determining protein functional specificity. Bioinformatics 24:1473-1480. (Pubitemid 351911698)
9. Casari G, Sander C, Valencia A. 1995. A method to predict functional residues in proteins. Nat Struct Biol. 2:171-178. (Pubitemid 26040653)
10. Chakrabarti S, Bryant SH, Panchenko AR. 2007. Functional specificity lies within the properties and evolutionary changes of amino acids. J Mol Biol. 373:801-810. (Pubitemid 47488404)
11. Chakrabarti S, Panchenko AR. 2009. Ensemble approach to predict specificity determinants: benchmarking and validation. BMC Bioinformatics 10:207.
12. Donald JE, Shakhnovich EI. 2009. SDR: a database of predicted specificitydetermining residues in proteins. Nucleic Acids Res. 37:D191-D194.
13. Edwards RJ, Shields DC. 2004. GASP: gapped ancestral sequence prediction for proteins. BMC Bioinformatics 5:123.
14. Eisen JA, Fraser CM. 2003. Phylogenomics: intersection of evolution and genomics. Science 300:1706-1707. (Pubitemid 36712558)
15. Gao X, Vander Velden KA, Voytas DF, Gu X. 2005. SplitTester: software to identify domains responsible for functional divergence in protein family. BMC Bioinformatics 6:137.
16. Gaucher EA, Gu X, Miyamoto MM, Benner SA. 2002. Predicting functional divergence in protein evolution by site-specific rate shifts. Trends Biochem Sci. 27:315-321. (Pubitemid 34628672)
17. Gu J, Wang Y, Gu X. 2002a. Evolutionary analysis for functional divergence of Jak protein kinase domains and tissue-specific genes. J Mol Evol. 54:725-733. (Pubitemid 34553638)
18. Gu X. 1999. Statistical methods for testing functional divergence after gene duplication. Mol Biol Evol. 16:1664-1674.
19. Gu X. 2001a. Maximum-likelihood approach for gene family evolution under functional divergence. Mol Biol Evol. 18:453-464. (Pubitemid 32267997)
20. Gu X. 2001b. A site-specific measure for rate difference after gene duplication or speciation. Mol Biol Evol. 18:2327-2330. (Pubitemid 33134363)
21. Gu X. 2003. Functional divergence in protein (family) sequence evolution. Genetica 118:133-141. (Pubitemid 36821045)
22. Gu X. 2006. A simple statistical method for estimating type-II (clusterspecific) functional divergence of protein sequences. Mol Biol Evol. 23:1937-1945. (Pubitemid 44412880)
23. Gu X. 2011. Statistical theory and methods for evolutionary genomics. Oxford: Oxford University Press.
24. 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. 40:464-473.
25. Gu X, Vander Velden K. 2002. DIVERGE: phylogeny-based analysis for functional-structural divergence of a protein family. Bioinformatics 18:500-501. (Pubitemid 34284959)
26. Gu X, Wang Y, Gu J. 2002b. Age distribution of human gene families shows significant roles of both large- and small-scale duplications in vertebrate evolution. Nat Genet. 31:205-209.
27. Gu X, Zhang J. 1997. A simple method for estimating the parameter of substitution rate variation among sites.Mol Biol Evol. 14:1106-1113. (Pubitemid 27463301)
28. Hannenhalli SS, Russell RB. 2000. Analysis and prediction of functional sub-types from protein sequence alignments. J Mol Biol. 303:61-76.
29. Huang Y, Zheng Y, Su Z, Gu X. 2009. Differences in duplication age distributions between human GPCRs and their downstream genes from a network prospective. BMC Genomics 10(1 suppl):S14.
30. Huang YF, Golding GB. 2011. Inferring sequence regions under functional divergence in duplicate genes. Bioinformatics 28:176-183.
31. Kalinina OV, Mironov AA, Gelfand MS, Rakhmaninova AB. 2004. Automated selection of positions determining functional specificity of proteins by comparative analysis of orthologous groups in protein families. Protein Sci. 13:443-456. (Pubitemid 38124965)
32. Kimura M. 1983. The neutral theory of molecular evolution. Cambridge: Cambridge University Press.
33. Knudsen B, Miyamoto MM. 2001. A likelihood ratio test for evolutionary rate shifts and functional divergence among proteins. Proc Natl Acad Sci U S A. 98:14512-14517. (Pubitemid 33121423)
34. Landgraf R, Xenarios I, Eisenberg D. 2001. Three-dimensional cluster analysis identifies interfaces and functional residue clusters in proteins. J Mol Biol. 307:1487-1502. (Pubitemid 33027653)
35. Lichtarge O, Bourne HR, Cohen FE. 1996. An evolutionary trace method defines binding surfaces common to protein families. J Mol Biol. 257: 342-358. (Pubitemid 26114038)
36. Lopez G, Valencia A, Tress M. 2007. FireDB-a database of functionally important residues from proteins of known structure. Nucleic Acids Res. 35:D219-D223. (Pubitemid 46056202)
37. Lopez P, Casane D, Philippe H. 2002. Heterotachy, an important process of protein evolution. Mol Biol Evol. 19:1-7. (Pubitemid 34008041)
38. Mertz B, Gu X, Reilly PJ. 2009. Analysis of functional divergence within two structurally related glycoside hydrolase families. Biopolymers 91: 478-495.
39. Ohno S. 1970. Evolution by gene duplication. Berlin (Germany): Springer-Verlag.
40. Pazos F, Rausell A, Valencia A. 2006. Phylogeny-independent detection of functional residues. Bioinformatics 22:1440-1448. (Pubitemid 43985314)
41. Pazos F, Sternberg MJ. 2004. Automated prediction of protein function and detection of functional sites from structure. Proc Natl Acad Sci U S A. 101:14754-14759. (Pubitemid 39410747)
42. Pupko T, Galtier N. 2002. A covarion-based method for detecting molecular adaptation: application to the evolution of primate mitochondrial genomes. Proc Biol Sci. 269:1313-1316. (Pubitemid 34753662)
43. Rausell A, Juan D, Pazos F, Valencia A. 2010. Protein interactions and ligand binding: from protein subfamilies to functional specificity. Proc Natl Acad Sci U S A. 107:1995-2000.
44. Reva B, Antipin Y, Sander C. 2007. Determinants of protein function revealed by combinatorial entropy optimization. Genome Biol. 8: R232.
45. Su Z, Gu X. 2012. Revisit on the evolutionary relationship between alternative splicing and gene duplication. Gene 504:102-106.
46. Su Z, HuangW, Gu X. 2011. Comment on "Positive selection of tyrosine loss in metazoan evolution." Science 332:917; author reply 917.
47. Su Z, Wang J, Yu J, Huang X, Gu X. 2006. Evolution of alternative splicing after gene duplication. Genome Res. 16:182-189. (Pubitemid 43200266)
48. Susko E, Inagaki Y, Field C, Holder ME, Roger AJ. 2002. Testing for differences in rates-across-sites distributions in phylogenetic subtrees. Mol Biol Evol. 19:1514-1523. (Pubitemid 36752776)
49. Tatusov RL, Koonin EV, Lipman DJ. 1997. A genomic perspective on protein families. Science 278:631-637. (Pubitemid 27464953)
50. Wallace IM, Higgins DG. 2007. Supervised multivariate analysis of sequence groups to identify specificity determining residues. BMC Bioinformatics 8:135.
51. Wang X, Huang Y, Lavrov DV, Gu X. 2009. Comparative study of human mitochondrial proteome reveals extensive protein subcellular relocalization after gene duplications. BMC Evol Biol. 9:275.
52. Wang Y, Gu X. 2001. Functional divergence in the caspase gene family and altered functional constraints: statistical analysis and prediction. Genetics 158:1311-1320. (Pubitemid 32667113)
53. Wolfe KH, Shields DC. 1997. Molecular evidence for an ancient duplication of the entire yeast genome. Nature 387:708-713. (Pubitemid 27270611)
54. Xia X. 2011. Comparative genomics. In: Lu HH-S, Schölkopf B, Zhao H, editors. Handbook of computational statistics: statistical bioinformatics. Berlin: Springer. p. 567-600.
55. Zheng Y, Xu D, Gu X. 2007. Functional divergence after gene duplication and sequence-structure relationship: a case study of G-protein alpha subunits. J Exp Zool B Mol Dev Evol. 308:85-96.
56. Zhou H, Gu J, Lamont SJ, Gu X. 2007. Evolutionary analysis for functional divergence of the toll-like receptor gene family and altered functional constraints. J Mol Evol. 65:119-123. (Pubitemid 47383772)
57. Zou Y, Huang W, Gu Z, Gu X. 2011. Predominant gain of promoter TATA box after gene duplication associated with stress responses. Mol Biol Evol. 28:2893-2904.
58. Zou Y, Su Z, Huang W, Gu X. 2012. Histone modification pattern evolution after yeast gene duplication. BMC Evol Biol. 12:111.