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Volumn 29, Issue 9, 2012, Pages 2133-2145

REvolver: Modeling sequence evolution under domain constraints

Author keywords

insertion; pHMM; protein domain; protein family; sequence simulation; site specific models

Indexed keywords

PROTEOME;

EID: 84865528220     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/mss078     Document Type: Article
Times cited : (11)

References (51)
  • 1
    • 33845904407 scopus 로고    scopus 로고
    • MtArt: A new model of amino acid replacement for Arthropoda
    • DOI 10.1093/molbev/msl136
    • Abascal F, Posada D, Zardoya R. 2007. MtArt: a new model of amino acid replacement for arthropoda. Mol Biol Evol. 24:1-5. (Pubitemid 46026273)
    • (2007) Molecular Biology and Evolution , vol.24 , Issue.1 , pp. 1-5
    • Abascal, F.1    Posada, D.2    Zardoya, R.3
  • 2
    • 0029974748 scopus 로고    scopus 로고
    • Model of amino acid substitution in proteins encoded by mitochondrial DNA
    • Adachi J, Hasegawa M. 1996. Model of amino acid substitution in proteins encoded by mitochondrial DNA. J Mol Evol. 42:459-468. (Pubitemid 26154323)
    • (1996) Journal of Molecular Evolution , vol.42 , Issue.4 , pp. 459-468
    • Adachi, J.1    Hasegawa, M.2
  • 3
    • 0033920569 scopus 로고    scopus 로고
    • Plastid genome phylogeny and a model of amino acid substitution for proteins encoded by chloroplast DNA
    • Adachi J, Waddell PJ, Martin W, Hasegawa M. 2000. Plastid genome phylogeny and a model of amino acid substitution for proteins encoded by chloroplast DNA. J Mol Evol. 50:348-358. (Pubitemid 30429968)
    • (2000) Journal of Molecular Evolution , vol.50 , Issue.4 , pp. 348-358
    • Adachi, J.1    Waddell, P.J.2    Martin, W.3    Hasegawa, M.4
  • 5
    • 0027483434 scopus 로고
    • Empirical and structural models for insertions and deletions in the divergent evolution of proteins
    • DOI 10.1006/jmbi.1993.1105
    • Benner SA, Cohen MA, Gonnet GH. 1993. Empirical and structural models for insertions and deletions in the divergent evolution of proteins. J Mol Biol. 229:1065-1082. (Pubitemid 23091821)
    • (1993) Journal of Molecular Biology , vol.229 , Issue.4 , pp. 1065-1082
    • Benner, S.A.1    Cohen, M.A.2    Gonnet, G.H.3
  • 6
    • 3342888069 scopus 로고    scopus 로고
    • Empirical analysis of protein insertions and deletions determining parameters for the correct placement of gaps in protein sequence alignments
    • DOI 10.1016/j.jmb.2004.05.045, PII S0022283604006151
    • Chang MSS, Benner SA. 2004. Empirical analysis of protein insertions and deletions determining parameters for the correct placement of gaps in protein sequence alignments. J Mol Biol. 341: 617-631. (Pubitemid 38987792)
    • (2004) Journal of Molecular Biology , vol.341 , Issue.2 , pp. 617-631
    • Chang, M.S.S.1    Benner, S.A.2
  • 7
    • 37849023306 scopus 로고    scopus 로고
    • Assessing performance of orthology detection strategies applied to eukaryotic genomes
    • Chen F, Mackey AJ, Vermunt JK, Roos DS. 2007. Assessing performance of orthology detection strategies applied to eukaryotic genomes. PloS One 2:e383.
    • (2007) PloS One , vol.2
    • Chen, F.1    MacKey, A.J.2    Vermunt, J.K.3    Roos, D.S.4
  • 9
    • 0031743421 scopus 로고    scopus 로고
    • Profile hidden Markov models
    • Eddy SR. 1998. Profile hidden Markov models. Bioinformatics 14:755-763. (Pubitemid 28552108)
    • (1998) Bioinformatics , vol.14 , Issue.9 , pp. 755-763
    • Eddy, S.R.1
  • 12
    • 75549090603 scopus 로고    scopus 로고
    • The Pfam protein families database
    • (14 co-authors)
    • Finn RD, Mistry J, Tate J, et al. (14 co-authors). 2010. The Pfam protein families database. Nucleic Acids Res. 38:D211-D222.
    • (2010) Nucleic Acids Res , vol.38
    • Finn, R.D.1    Mistry, J.2    Tate, J.3
  • 13
    • 67749108209 scopus 로고    scopus 로고
    • INDELible: A flexible simulator of biological sequence evolution
    • Fletcher W, Yang Z. 2009. INDELible: a flexible simulator of biological sequence evolution. Mol Biol Evol. 26:1879-1888.
    • (2009) Mol Biol Evol , vol.26 , pp. 1879-1888
    • Fletcher, W.1    Yang, Z.2
  • 14
    • 48249113702 scopus 로고    scopus 로고
    • Predicting protein function from domain content
    • Forslund K, Sonnhammer ELL. 2008. Predicting protein function from domain content. Bioinformatics 24:1681-1687.
    • (2008) Bioinformatics , vol.24 , pp. 1681-1687
    • Forslund, K.1    Sonnhammer, E.L.L.2
  • 15
    • 33645429016 scopus 로고
    • Exact stochastic simulation of coupled chemical reactions
    • Gillespie DT. 1977. Exact stochastic simulation of coupled chemical reactions. J Phys Chem. 81:2340-2361.
    • (1977) J Phys Chem , vol.81 , pp. 2340-2361
    • Gillespie, D.T.1
  • 16
    • 82955187769 scopus 로고    scopus 로고
    • Fast side chain replacement in proteins using a coarse-grained approach for evaluating the effects of mutation during evolution
    • Grahnen JA, Kubelka J, Liberles DA. 2011. Fast side chain replacement in proteins using a coarse-grained approach for evaluating the effects of mutation during evolution. J Mol Evol. 73:23-33.
    • (2011) J Mol Evol , vol.73 , pp. 23-33
    • Grahnen, J.A.1    Kubelka, J.2    Liberles, D.A.3
  • 17
    • 83455238341 scopus 로고    scopus 로고
    • Biophysical and structural considerations for protein sequence evolution
    • Grahnen JA, Nandakumar P, Kubelka J, Liberles DA. 2011. Biophysical and structural considerations for protein sequence evolution. BMC Evol Biol. 11:361.
    • (2011) BMC Evol Biol , vol.11 , pp. 361
    • Grahnen, J.A.1    Nandakumar, P.2    Kubelka, J.3    Liberles, D.A.4
  • 18
    • 0026458378 scopus 로고
    • Amino acid substitution matrices from protein blocks
    • Henikoff S, Henikoff JG. 1992. Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci USA. 89:10915-10919.
    • (1992) Proc Natl Acad Sci USA , vol.89 , pp. 10915-10919
    • Henikoff, S.1    Henikoff, J.G.2
  • 19
    • 0026691182 scopus 로고
    • The rapid generation of mutation data matrices from protein sequences
    • Jones DT, Taylor WR, Thornton JM. 1992. The rapid generation of mutation data matrices from protein sequences. CABIOS 8:275-282.
    • (1992) CABIOS , vol.8 , pp. 275-282
    • Jones, D.T.1    Taylor, W.R.2    Thornton, J.M.3
  • 21
    • 76949098763 scopus 로고    scopus 로고
    • Towards realistic benchmarks for multiple alignments of non-coding sequences
    • Kim J, Sinha S. 2010. Towards realistic benchmarks for multiple alignments of non-coding sequences. BMC Bioinformatics. 11:54.
    • (2010) BMC Bioinformatics , vol.11 , pp. 54
    • Kim, J.1    Sinha, S.2
  • 22
    • 77955290742 scopus 로고    scopus 로고
    • FACT: Functional annotation transfer between proteins with similar feature architectures
    • Koestler T, von Haeseler A, Ebersberger I. 2010. FACT: functional annotation transfer between proteins with similar feature architectures. BMC Bioinformatics. 11:417.
    • (2010) BMC Bioinformatics , vol.11 , pp. 417
    • Koestler, T.1    Von Haeseler, A.2    Ebersberger, I.3
  • 23
    • 12344269158 scopus 로고    scopus 로고
    • Different versions of the dayhoff rate matrix
    • DOI 10.1093/molbev/msi005
    • Kosiol C, Goldman N. 2005. Different versions of the dayhoff rate matrix. Mol Biol Evol. 22:193-199. (Pubitemid 40130187)
    • (2005) Molecular Biology and Evolution , vol.22 , Issue.2 , pp. 193-199
    • Kosiol, C.1    Goldman, N.2
  • 24
    • 0035253047 scopus 로고    scopus 로고
    • Zinc finger proteins: New insights into structural and functional diversity
    • DOI 10.1016/S0959-440X(00)00167-6
    • Laity JH, Lee BM, Wright PE. 2001. Zinc finger proteins: new insights into structural and functional diversity. Curr Opin Struct Biol. 11:39-46. (Pubitemid 32155550)
    • (2001) Current Opinion in Structural Biology , vol.11 , Issue.1 , pp. 39-46
    • Laity, J.H.1    Lee, B.M.2    Wright, P.E.3
  • 25
    • 79951566879 scopus 로고    scopus 로고
    • What's in a likelihood? Simple models of protein evolution and the contribution of structurally viable reconstructions to the likelihood
    • Lakner C, Holder MT, Goldman N, Naylor GJP. 2011. What's in a likelihood? Simple models of protein evolution and the contribution of structurally viable reconstructions to the likelihood. Syst Biol. 60:161-174.
    • (2011) Syst Biol , vol.60 , pp. 161-174
    • Lakner, C.1    Holder, M.T.2    Goldman, N.3    Naylor, G.J.P.4
  • 26
    • 45849154166 scopus 로고    scopus 로고
    • An improved general amino acid replacement matrix
    • DOI 10.1093/molbev/msn067
    • Le SQ, Gascuel O. 2008. An improved general amino acid replacement matrix. Mol Biol Evol. 25:1307-1320. (Pubitemid 351882003)
    • (2008) Molecular Biology and Evolution , vol.25 , Issue.7 , pp. 1307-1320
    • Le, S.Q.1    Gascuel, O.2
  • 27
    • 58149194624 scopus 로고    scopus 로고
    • SMART 6: Recent updates and new developments
    • Letunic I, Doerks T, Bork P. 2009. SMART 6: recent updates and new developments. Nucleic Acids Res. 37:D229-D232.
    • (2009) Nucleic Acids Res , vol.37
    • Letunic, I.1    Doerks, T.2    Bork, P.3
  • 28
    • 0034922289 scopus 로고    scopus 로고
    • Modeling amino acid replacement
    • DOI 10.1089/10665270050514918
    • Muller T, Vingron M. 2000. Modeling amino acid replacement. J Comput Biol A J Comput Mol Cell Biol. 7:761-776. (Pubitemid 32692448)
    • (2001) Journal of Computational Biology , vol.7 , Issue.6 , pp. 761-776
    • Muller, T.1    Vingron, M.2
  • 30
    • 34548400364 scopus 로고    scopus 로고
    • Recent evolutions of multiple sequence alignment algorithms
    • Notredame C. 2007. Recent evolutions of multiple sequence alignment algorithms. PLoS Comput Biol. 3:e123.
    • (2007) PLoS Comput Biol , vol.3
    • Notredame, C.1
  • 32
    • 27644471132 scopus 로고    scopus 로고
    • SIMPROT: Using an empirically determined indel distribution in simulations of protein evolution
    • Pang A, Smith AD, Nuin PAS, Tillier ERM. 2005. SIMPROT: using an empirically determined indel distribution in simulations of protein evolution. BMC Bioinformatics. 6:236.
    • (2005) BMC Bioinformatics , vol.6 , pp. 236
    • Pang, A.1    Smith, A.D.2    Nuin, P.A.S.3    Tillier, E.R.M.4
  • 33
    • 0035028705 scopus 로고    scopus 로고
    • Structural constraints and emergence of sequence patterns in protein evolution
    • Parisi G, Echave J. 2001. Structural constraints and emergence of sequence patterns in protein evolution. Mol Biol Evol. 18:750-756. (Pubitemid 32372945)
    • (2001) Molecular Biology and Evolution , vol.18 , Issue.5 , pp. 750-756
    • Parisi, G.1    Echave, J.2
  • 34
    • 0033212986 scopus 로고    scopus 로고
    • Crystal structures of the XLP protein SAP reveal a class of SH2 domains with extended, phosphotyrosine-independent sequence recognition
    • DOI 10.1016/S1097-2765(00)80206-3
    • Poy F, Yaffe MB, Sayos J, Saxena K, Morra M, Sumegi J, Cantley LC, Terhorst C, Eck MJ. 1999. Crystal structures of the XLP protein SAP reveal a class of SH2 domains with extended, phosphotyrosineindependent sequence recognition. Mol Cell. 4:555-561. (Pubitemid 29531135)
    • (1999) Molecular Cell , vol.4 , Issue.4 , pp. 555-561
    • Poy, F.1    Yaffe, M.B.2    Sayos, J.3    Saxena, K.4    Morra, M.5    Sumegi, J.6    Cantley, L.C.7    Terhorst, C.8    Eck, M.J.9
  • 35
    • 0030928378 scopus 로고    scopus 로고
    • Seq-gen: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees
    • Rambaut A, Grassly NC. 1997. Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. CABIOS 13:235-238. (Pubitemid 27249927)
    • (1997) Computer Applications in the Biosciences , vol.13 , Issue.3 , pp. 235-238
    • Rambaut, A.1    Grassly, N.C.2
  • 36
    • 33750180978 scopus 로고    scopus 로고
    • Evaluation of models for the evolution of protein sequences and functions under structural constraint
    • DOI 10.1016/j.bpc.2006.06.008, PII S0301462206002080
    • Rastogi S, Reuter N, Liberles DA. 2006. Evaluation of models for the evolution of protein sequences and functions under structural constraint. Biophys Chem. 124:134-144. (Pubitemid 44602326)
    • (2006) Biophysical Chemistry , vol.124 , Issue.2 , pp. 134-144
    • Rastogi, S.1    Reuter, N.2    Liberles, D.A.3
  • 37
    • 0035861990 scopus 로고    scopus 로고
    • Automatic clustering of orthologs and in-paralogs from pairwise species comparisons
    • DOI 10.1006/jmbi.2000.5197
    • Remm M, Storm CE, Sonnhammer EL. 2001. Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. J Mol Biol. 314:1041-1052. (Pubitemid 34073068)
    • (2001) Journal of Molecular Biology , vol.314 , Issue.5 , pp. 1041-1052
    • Remm, M.1    Storm, C.E.V.2    Sonnhammer, E.L.L.3
  • 39
    • 16344373015 scopus 로고    scopus 로고
    • Protein homology detection by HMM-HMM comparison
    • Sding J. 2005. Protein homology detection by HMM-HMM comparison. Bioinformatics 21:951-960.
    • (2005) Bioinformatics , vol.21 , pp. 951-960
    • Sding, J.1
  • 40
    • 0031857684 scopus 로고    scopus 로고
    • Rose: Generating sequence families
    • Stoye J, Evers D, Meyer F. 1998. Rose: generating sequence families. Bioinformatics 14:157-163. (Pubitemid 28395875)
    • (1998) Bioinformatics , vol.14 , Issue.2 , pp. 157-163
    • Stoye, J.1    Evers, D.2    Meyer, F.3
  • 41
    • 73349096292 scopus 로고    scopus 로고
    • Biological sequence simulation for testing complex evolutionary hypotheses: Indel-Seq-Gen version 2.0
    • Strope CL, Abel K, Scott SD, Moriyama EN. 2009. Biological sequence simulation for testing complex evolutionary hypotheses: indel-Seq-Gen version 2.0. Mol Biol Evol. 26:2581-2593.
    • (2009) Mol Biol Evol , vol.26 , pp. 2581-2593
    • Strope, C.L.1    Abel, K.2    Scott, S.D.3    Moriyama, E.N.4
  • 42
    • 33847668252 scopus 로고    scopus 로고
    • Indel-Seq-Gen: A new protein family simulator incorporating domains, motifs, and indels
    • DOI 10.1093/molbev/msl195
    • Strope CL, Scott SD, Moriyama EN. 2007. indel-Seq-Gen: a new protein family simulator incorporating domains, motifs, and indels. Mol Biol Evol. 24:640-649. (Pubitemid 46355791)
    • (2007) Molecular Biology and Evolution , vol.24 , Issue.3 , pp. 640-649
    • Strope, C.L.1    Scott, S.D.2    Moriyama, E.N.3
  • 43
    • 78651319979 scopus 로고    scopus 로고
    • Ongoing and future developments at the universal protein resource
    • The UniProt Consortium
    • The UniProt Consortium. 2010. Ongoing and future developments at the universal protein resource. Nucleic Acids Res. 39: D214-D219.
    • (2010) Nucleic Acids Res , vol.39
  • 44
    • 0026079507 scopus 로고
    • An evolutionary model for maximum likelihood alignment of DNA sequences
    • Thorne JL, Kishino H, Felsenstein J. 1991. An evolutionary model for maximum likelihood alignment of DNA sequences. J Mol Evol. 33:114-124.
    • (1991) J Mol Evol , vol.33 , pp. 114-124
    • Thorne, J.L.1    Kishino, H.2    Felsenstein, J.3
  • 45
    • 0034786532 scopus 로고    scopus 로고
    • The HMMTOP transmembrane topology prediction server
    • Tusndy GE, Simon I. 2001. The HMMTOP transmembrane topology prediction server. Bioinformatics 17 849-850. (Pubitemid 32970487)
    • (2001) Bioinformatics , vol.17 , Issue.9 , pp. 849-850
    • Tusnady, G.E.1    Simon, I.2
  • 46
    • 78651300218 scopus 로고    scopus 로고
    • PDBe: Protein data bank in Europe
    • (33 co-authors)
    • Velankar S, Alhroub Y, Alili A, et al. (33 co-authors). 2011. PDBe: protein data bank in europe. Nucleic Acids Res. 39:D402-D410.
    • (2011) Nucleic Acids Res , vol.39
    • Velankar, S.1    Alhroub, Y.2    Alili, A.3
  • 47
    • 84935113569 scopus 로고
    • Error bounds for convolutional codes and an asymptotically optimum decoding algorithm
    • Viterbi A. 1967. Error bounds for convolutional codes and an asymptotically optimum decoding algorithm. IEEE Trans Inf Theory. 13:260-269.
    • (1967) IEEE Trans Inf Theory , vol.13 , pp. 260-269
    • Viterbi, A.1
  • 48
    • 0031901451 scopus 로고    scopus 로고
    • Evolution of DNA or amino acid sequences with dependent sites
    • von Haeseler A, Schniger M. 1998. Evolution of DNA or amino acid sequences with dependent sites. J Comput Biol A J Comput Mol Cell Biol. 5:149-163. (Pubitemid 28153012)
    • (1998) Journal of Computational Biology , vol.5 , Issue.1 , pp. 149-163
    • Von Haeseler, A.1    Schoniger, M.2
  • 49
    • 0035031966 scopus 로고    scopus 로고
    • A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach
    • Whelan S, Goldman N. 2001.Ageneral empirical model of protein evolution derived from multiple protein families using a maximumlikelihood approach. Mol Biol Evol. 18:691-699. (Pubitemid 32372940)
    • (2001) Molecular Biology and Evolution , vol.18 , Issue.5 , pp. 691-699
    • Whelan, S.1    Goldman, N.2
  • 51
    • 0031792828 scopus 로고    scopus 로고
    • Models of amino acid substitution and applications to mitochondrial protein evolution
    • Yang Z, Nielsen R, Hasegawa M. 1998. Models of amino acid substitution and applications to mitochondrial protein evolution. Mol Biol Evol. 15:1600-1611. (Pubitemid 28550985)
    • (1998) Molecular Biology and Evolution , vol.15 , Issue.12 , pp. 1600-1611
    • Yang, Z.1    Nielsen, R.2    Hasegawa, M.3


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