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Volumn 28, Issue 2, 2012, Pages 176-183

Inferring sequence regions under functional divergence in duplicate genes

Author keywords

[No Author keywords available]

Indexed keywords

ANIMALIA;

EID: 84862964759     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btr635     Document Type: Article
Times cited : (10)

References (48)
  • 1
    • 13444302764 scopus 로고    scopus 로고
    • FunShift: a database of function shift analysis on protein subfamilies
    • Abhiman,S. and Sonnhammer,E.L. (2005a) FunShift: a database of function shift analysis on protein subfamilies. Nucleic Acids Res., 33, D197-D200.
    • (2005) Nucleic Acids Res , vol.33
    • Abhiman, S.1    Sonnhammer, E.L.2
  • 2
    • 24644447811 scopus 로고    scopus 로고
    • Large-scale prediction of function shift in protein families with a focus on enzymatic function
    • Abhiman,S. and Sonnhammer,E.L. (2005b) Large-scale prediction of function shift in protein families with a focus on enzymatic function. Proteins, 60, 758-768.
    • (2005) Proteins , vol.60 , pp. 758-768
    • Abhiman, S.1    Sonnhammer, E.L.2
  • 3
    • 33748974481 scopus 로고    scopus 로고
    • Uvpar: fast detection of functional shifts in duplicate genes
    • Arnau,V. et al. (2006) Uvpar: fast detection of functional shifts in duplicate genes. BMC Bioinformatics, 7, 174.
    • (2006) BMC Bioinformatics , vol.7 , pp. 174
    • Arnau, V.1
  • 4
    • 0031467960 scopus 로고    scopus 로고
    • Molecular determinants of selectivity in 5-hydroxytryptamine1b receptor-g protein interactions
    • Bae,H. et al. (1997) Molecular determinants of selectivity in 5-hydroxytryptamine1b receptor-g protein interactions. J. Biol. Chem., 272, 32071-32077.
    • (1997) J. Biol. Chem. , vol.272 , pp. 32071-32077
    • Bae, H.1
  • 5
    • 0033591051 scopus 로고    scopus 로고
    • Two amino acids within the α4 helix of Gi1 mediate coupling with 5-Hydroxytryptamine1B receptors
    • Bae,H. et al. (1999) Two amino acids within the α4 helix of Gi1 mediate coupling with 5-Hydroxytryptamine1B receptors. J. Biol. Chem., 274, 14963-14971.
    • (1999) J. Biol. Chem. , vol.274 , pp. 14963-14971
    • Bae, H.1
  • 6
    • 0037270595 scopus 로고    scopus 로고
    • Maximum likelihood methods for detecting adaptive evolution after gene duplication
    • Bielawski,J.P. and Yang,Z. (2003) Maximum likelihood methods for detecting adaptive evolution after gene duplication. J. Struct. Funct. Genomics, 3, 201-212.
    • (2003) J. Struct. Funct. Genomics , vol.3 , pp. 201-212
    • Bielawski, J.P.1    Yang, Z.2
  • 7
    • 0037440008 scopus 로고    scopus 로고
    • Inferring functional constraints and divergence in protein families using 3D mapping of phylogenetic information
    • Blouin,C. et al. (2003) Inferring functional constraints and divergence in protein families using 3D mapping of phylogenetic information. Nucleic Acids Res., 31, 790-797.
    • (2003) Nucleic Acids Res , vol.31 , pp. 790-797
    • Blouin, C.1
  • 8
    • 0347949548 scopus 로고    scopus 로고
    • Insights into G protein structure, function, and regulation
    • Cabrera-Vera,T.M. et al. (2003) Insights into G protein structure, function, and regulation. Endocrine Rev., 24, 765-781.
    • (2003) Endocrine Rev. , vol.24 , pp. 765-781
    • Cabrera-Vera, T.M.1
  • 9
    • 79952258986 scopus 로고    scopus 로고
    • Correlated evolution of nearby residues in drosophilid proteins
    • Callahan,B. et al. (2011) Correlated evolution of nearby residues in drosophilid proteins. PLoS Genet., 7, e1001315.
    • (2011) PLoS Genet. , vol.7
    • Callahan, B.1
  • 10
    • 1342288004 scopus 로고    scopus 로고
    • The Jalview java alignment editor
    • Clamp,M. et al. (2004) The Jalview java alignment editor. Bioinformatics, 20, 426-427.
    • (2004) Bioinformatics , vol.20 , pp. 426-427
    • Clamp, M.1
  • 11
    • 34248157297 scopus 로고    scopus 로고
    • Identifying dramatic selection shifts in phylogenetic trees
    • Dorman,K. (2007) Identifying dramatic selection shifts in phylogenetic trees. BMC Evol. Biol., 7, S10.
    • (2007) BMC Evol. Biol. , vol.7
    • Dorman, K.1
  • 12
    • 0003516147 scopus 로고    scopus 로고
    • Cambridge University Press, Cambridge, UK
    • Durbin,R. et al. (1998) Biological Sequence Analysis. Cambridge University Press, Cambridge, UK.
    • (1998) Biological Sequence Analysis
    • Durbin, R.1
  • 13
    • 33745955637 scopus 로고    scopus 로고
    • Bio++: A set of C++ libraries for sequence analysis, phylogenetics, molecular evolution and population genetics
    • Dutheil,J. et al. (2006) Bio++: A set of C++ libraries for sequence analysis, phylogenetics, molecular evolution and population genetics. BMC Bioinformatics, 7, 188.
    • (2006) BMC Bioinformatics , vol.7 , pp. 188
    • Dutheil, J.1
  • 14
    • 3042666256 scopus 로고    scopus 로고
    • MUSCLE: multiple sequence alignment with high accuracy and high throughput
    • Edgar,R.C. (2004)MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res., 32, 1792-1797.
    • (2004) Nucleic Acids Res. , vol.32 , pp. 1792-1797
    • Edgar, R.C.1
  • 15
    • 0019797407 scopus 로고
    • Evolutionary trees from DNA sequences: a maximum likelihood approach
    • Felsenstein,J. (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol., 17, 368-376.
    • (1981) J. Mol. Evol. , vol.17 , pp. 368-376
    • Felsenstein, J.1
  • 16
    • 25444453179 scopus 로고    scopus 로고
    • SplitTester: Software to identify domains responsible for functional divergence in protein family
    • Gao,X. et al. (2005) SplitTester: Software to identify domains responsible for functional divergence in protein family. BMC Bioinformatics, 6, 137.
    • (2005) BMC Bioinformatics , vol.6 , pp. 137
    • Gao, X.1
  • 17
    • 0031966661 scopus 로고    scopus 로고
    • The structural basis of molecular adaptation
    • Golding,G.B. and Dean,A.M. (1998) The structural basis of molecular adaptation. Mol. Biol. Evol., 15, 355-369.
    • (1998) Mol. Biol. Evol. , vol.15 , pp. 355-369
    • Golding, G.B.1    Dean, A.M.2
  • 18
    • 0242666374 scopus 로고    scopus 로고
    • Functional divergence prediction from evolutionary analysis: a case study of vertebrate hemoglobin
    • Gribaldo,S. et al. (2003) Functional divergence prediction from evolutionary analysis: a case study of vertebrate hemoglobin. Mol. Biol. Evol., 20, 1754-1759.
    • (2003) Mol. Biol. Evol. , vol.20 , pp. 1754-1759
    • Gribaldo, S.1
  • 19
    • 0032728408 scopus 로고    scopus 로고
    • Statistical methods for testing functional divergence after gene duplication
    • Gu,X. (1999) Statistical methods for testing functional divergence after gene duplication. Mol. Biol. Evol., 16, 1664-1674.
    • (1999) Mol. Biol. Evol. , vol.16 , pp. 1664-1674
    • Gu, X.1
  • 20
    • 0035061686 scopus 로고    scopus 로고
    • Maximum-likelihood approach for gene family evolution under functional divergence
    • Gu,X. (2001a) Maximum-likelihood approach for gene family evolution under functional divergence. Mol. Biol. Evol., 18, 453-464.
    • (2001) Mol. Biol. Evol. , vol.18 , pp. 453-464
    • Gu, X.1
  • 21
    • 0035211809 scopus 로고    scopus 로고
    • A site-specic measure for rate difference after gene duplication or speciation
    • Gu,X. (2001b) A site-specic measure for rate difference after gene duplication or speciation. Mol. Biol. Evol., 18, 2327-2330.
    • (2001) Mol. Biol. Evol. , vol.18 , pp. 2327-2330
    • Gu, X.1
  • 22
    • 33748784344 scopus 로고    scopus 로고
    • A simple statistical method for estimating Type-II (cluster-specic) functional divergence of protein sequences
    • Gu,X. (2006) A simple statistical method for estimating Type-II (cluster-specic) functional divergence of protein sequences. Mol. Biol. Evol., 23, 1937-1945.
    • (2006) Mol. Biol. Evol. , vol.23 , pp. 1937-1945
    • Gu, X.1
  • 23
    • 0242578620 scopus 로고    scopus 로고
    • A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood
    • Guindon,S. and Gascuel,O. (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol., 52, 696-704.
    • (2003) Syst. Biol. , vol.52 , pp. 696-704
    • Guindon, S.1    Gascuel, O.2
  • 24
    • 0026691182 scopus 로고
    • The rapid generation of mutation data matrices from protein sequences
    • Jones,D.T. et al. (1992) The rapid generation of mutation data matrices from protein sequences. Comput. Appl. Biosci., 8, 275-282.
    • (1992) Comput. Appl. Biosci. , vol.8 , pp. 275-282
    • Jones, D.T.1
  • 25
    • 0025910365 scopus 로고
    • Structure and function of signal-transducing GTP-binding proteins
    • Kaziro,Y. et al. (1991) Structure and function of signal-transducing GTP-binding proteins. Annu. Rev. Biochem., 60, 349-400.
    • (1991) Annu. Rev. Biochem. , vol.60 , pp. 349-400
    • Kaziro, Y.1
  • 26
    • 0035807886 scopus 로고    scopus 로고
    • A likelihood ratio test for evolutionary rate shifts and functional divergence among proteins
    • Knudsen,B. and Miyamoto,M. M. (2001) A likelihood ratio test for evolutionary rate shifts and functional divergence among proteins. Proc. Natl Acad. Sci. USA, 98, 14512-14517.
    • (2001) Proc. Natl Acad. Sci. USA , vol.98 , pp. 14512-14517
    • Knudsen, B.1    Miyamoto, M.M.2
  • 27
    • 0041817651 scopus 로고    scopus 로고
    • Using evolutionary rates to investigate protein functional divergence and conservation: a case study of the carbonic anhydrases
    • Knudsen,B. et al. (2003) Using evolutionary rates to investigate protein functional divergence and conservation: a case study of the carbonic anhydrases. Genetics, 164, 1261-1269.
    • (2003) Genetics , vol.164 , pp. 1261-1269
    • Knudsen, B.1
  • 28
    • 0028237708 scopus 로고
    • Structural determinants for activation of the α-subunit of a heterotrimeric g protein
    • Lambright,D.G. et al. (1994) Structural determinants for activation of the α-subunit of a heterotrimeric g protein. Nature, 369, 621-628.
    • (1994) Nature , vol.369 , pp. 621-628
    • Lambright, D.G.1
  • 29
    • 0029106731 scopus 로고
    • Multiple regions of G alpha 16 contribute to the specicity of activation by the C5a receptor
    • Lee,C.H. et al. (1995) Multiple regions of G alpha 16 contribute to the specicity of activation by the C5a receptor. Mol. Pharmacol., 47, 218-223.
    • (1995) Mol. Pharmacol. , vol.47 , pp. 218-223
    • Lee, C.H.1
  • 30
    • 0035140949 scopus 로고    scopus 로고
    • Detecting changes in the functional constraints of paralogous genes
    • Marin,I. et al. (2001) Detecting changes in the functional constraints of paralogous genes. J. Mol. Evol., 52, 17-28.
    • (2001) J. Mol. Evol. , vol.52 , pp. 17-28
    • Marin, I.1
  • 31
    • 27944465615 scopus 로고    scopus 로고
    • A simple method for predicting the functional differentiation of duplicate genes and its application to MIKC-type MADS-box genes
    • Nam,J. et al. (2005) A simple method for predicting the functional differentiation of duplicate genes and its application to MIKC-type MADS-box genes. Nucleic Acids Res., 33, e12.
    • (2005) Nucleic Acids Res. , vol.33
    • Nam, J.1
  • 32
    • 0028860268 scopus 로고
    • Heterotrimeric G proteins: organizers of transmembrane signals
    • Neer,E.J. (1995) Heterotrimeric G proteins: organizers of transmembrane signals. Cell, 80, 249-257.
    • (1995) Cell , vol.80 , pp. 249-257
    • Neer, E.J.1
  • 33
    • 78649590887 scopus 로고    scopus 로고
    • Bayesian classication of residues associated with protein functional divergence: Arf and Arf-like GTPases
    • Neuwald,A. (2010) Bayesian classication of residues associated with protein functional divergence: Arf and Arf-like GTPases. Biol. Direct, 5, 66.
    • (2010) Biol. Direct , vol.5 , pp. 66
    • Neuwald, A.1
  • 34
    • 84862913518 scopus 로고
    • Numerical Recipes in C, 2nd edn. Cambridge University Press, New York USA
    • Press,W. et al. (1992) Numerical Recipes in C, 2nd edn. Cambridge University Press, New York, USA.
    • (1992)
    • Press, W.1
  • 35
    • 0037036501 scopus 로고    scopus 로고
    • A covarion-based method for detecting molecular adaptation: Application to the evolution of primate mitochondrial genomes
    • Pupko,T. and Galtier,N. (2002) A covarion-based method for detecting molecular adaptation: Application to the evolution of primate mitochondrial genomes. Proc. R. Soc. Lond. B Biol. Sci., 269, 1313-1316.
    • (2002) Proc. R. Soc. Lond. B Biol. Sci. , vol.269 , pp. 1313-1316
    • Pupko, T.1    Galtier, N.2
  • 36
    • 77958514257 scopus 로고    scopus 로고
    • Positive selection differs between protein secondary structure elements in Drosophila
    • Ridout,K.E. et al. (2010). Positive selection differs between protein secondary structure elements in Drosophila. Genome Biol. Evol., 2, 166-179.
    • (2010) Genome Biol. Evol. , vol.2 , pp. 166-179
    • Ridout, K.E.1
  • 37
    • 56749103771 scopus 로고    scopus 로고
    • The trouble with sliding windows and the selective pressure in BRCA1
    • Schmid,K. and Yang,Z. (2008) The trouble with sliding windows and the selective pressure in BRCA1. PLoS One, 3, e3746.
    • (2008) PLoS One , vol.3
    • Schmid, K.1    Yang, Z.2
  • 38
    • 1542537849 scopus 로고    scopus 로고
    • Combining phylogenetic and hidden markov models in biosequence analysis
    • Siepel,A. and Haussler,D. (2004) Combining phylogenetic and hidden markov models in biosequence analysis. J. Comput. Biol., 11, 413-428.
    • (2004) J. Comput. Biol. , vol.11 , pp. 413-428
    • Siepel, A.1    Haussler, D.2
  • 39
    • 17644409239 scopus 로고    scopus 로고
    • Phylogenetic hidden markov models
    • Nielsen,R. (ed.). Statistics for Biology and Health, Chapter 12 Springer, New York Statistical Methods in Molecular Evolution
    • Siepel,A. and Haussler,D. (2005) Phylogenetic hidden markov models. In Nielsen,R. (ed.) Statistical Methods in Molecular Evolution. Statistics for Biology and Health, Chapter 12. Springer, New York, pp. 325-351.
    • (2005) , pp. 325-351
    • Siepel, A.1    Haussler, D.2
  • 40
    • 33745772571 scopus 로고    scopus 로고
    • New methods for detecting lineage-specic selection
    • Siepel,A. et al. (2006) New methods for detecting lineage-specic selection. Lect. Notes Comput. Sc., 3909, 190-205.
    • (2006) Lect. Notes Comput. Sc. , vol.3909 , pp. 190-205
    • Siepel, A.1
  • 41
    • 0025834532 scopus 로고
    • Diversity of G proteins in signal transduction
    • Simon,M. et al. (1991) Diversity of G proteins in signal transduction. Science, 252, 802-808.
    • (1991) Science , vol.252 , pp. 802-808
    • Simon, M.1
  • 42
    • 27544491192 scopus 로고    scopus 로고
    • ROCR: visualizing classier performance in R
    • Sing,T. et al. (2005) ROCR: visualizing classier performance in R. Bioinformatics, 21, 3940-3941.
    • (2005) Bioinformatics , vol.21 , pp. 3940-3941
    • Sing, T.1
  • 43
    • 0036730253 scopus 로고    scopus 로고
    • Testing for differences in rates-across-sites distributions in phylogenetic subtrees
    • Susko,E. et al. (2002) Testing for differences in rates-across-sites distributions in phylogenetic subtrees. Mol. Biol. Evol., 19, 1514-1523.
    • (2002) Mol. Biol. Evol. , vol.19 , pp. 1514-1523
    • Susko, E.1
  • 44
    • 0028064845 scopus 로고
    • Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods
    • Yang,Z. (1994) Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods. J. Mol. Evol., 39, 306-314.
    • (1994) J. Mol. Evol. , vol.39 , pp. 306-314
    • Yang, Z.1
  • 45
    • 0028813337 scopus 로고
    • A space-time process model for the evolution of DNA sequences
    • Yang,Z. (1995) A space-time process model for the evolution of DNA sequences. Genetics, 139, 993-1005.
    • (1995) Genetics , vol.139 , pp. 993-1005
    • Yang, Z.1
  • 47
    • 67650899071 scopus 로고    scopus 로고
    • Maximum-likelihood model averaging to prole clustering of site types across discrete linear sequences
    • Zhang,Z. and Townsend,J.P. (2009) Maximum-likelihood model averaging to prole clustering of site types across discrete linear sequences. PLoS Comput. Biol., 5, e1000421.
    • (2009) PLoS Comput. Biol. , vol.5
    • Zhang, Z.1    Townsend, J.P.2
  • 48
    • 33847238811 scopus 로고    scopus 로고
    • Functional divergence after gene duplication and sequence-structure relationship: a case study of G-protein alpha subunits
    • Zheng,Y. et al. (2007) Functional divergence after gene duplication and sequence-structure relationship: a case study of G-protein alpha subunits. J. Exp. Zoolog. B Mol. Dev. Evol., 308, 85-96
    • (2007) J. Exp. Zoolog. B Mol. Dev. Evol. , vol.308 , pp. 85-96
    • Zheng, Y.1


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