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Volumn 42, Issue 2, 2007, Pages 298-307

Modeling amino acid substitution patterns in orthologous and paralogous genes

Author keywords

Amino acid substitution; Evolutionary models; Protein evolution

Indexed keywords

ACTIN; AMINO ACID; HEMOGLOBIN; MYOSIN; OPSIN; RHODOPSIN;

EID: 33750992513     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2006.07.006     Document Type: Article
Times cited : (37)

References (44)
  • 2
    • 0030801002 scopus 로고    scopus 로고
    • Gapped blast and psi-blast: a new-generation of protein database search programs
    • Altschul S.F., Madden T.L., Schaffer A.A., et al. Gapped blast and psi-blast: a new-generation of protein database search programs. Nucleic Acids Res. 25 (1997) 3389-3402
    • (1997) Nucleic Acids Res. , vol.25 , pp. 3389-3402
    • Altschul, S.F.1    Madden, T.L.2    Schaffer, A.A.3
  • 3
    • 0034897709 scopus 로고    scopus 로고
    • Accuracy and power of the likelihood ratio test in detecting adaptive molecular evolution
    • Anisimova M., Bielawski J.P., and Yang Z. Accuracy and power of the likelihood ratio test in detecting adaptive molecular evolution. Mol. Biol. Evol. 18 (2001) 1585-1592
    • (2001) Mol. Biol. Evol. , vol.18 , pp. 1585-1592
    • Anisimova, M.1    Bielawski, J.P.2    Yang, Z.3
  • 4
    • 4544252051 scopus 로고    scopus 로고
    • Gene phylogenies and protein-protein interactions: possible artifacts resulting from shared protein interaction partners
    • Campos P.R.A., Olivera V.M., Wagner G.P., and Stadler P.F. Gene phylogenies and protein-protein interactions: possible artifacts resulting from shared protein interaction partners. J. Theor. Biol. 231 (2004) 197-202
    • (2004) J. Theor. Biol. , vol.231 , pp. 197-202
    • Campos, P.R.A.1    Olivera, V.M.2    Wagner, G.P.3    Stadler, P.F.4
  • 5
    • 0002929101 scopus 로고
    • A model of evolutionary change in proteins
    • Dayhoff M.O. (Ed), National Biomedical Research Foundation, Washington, DC
    • Dayhoff M.O., Eck R.V., and Park C.M. A model of evolutionary change in proteins. In: Dayhoff M.O. (Ed). Atlas of Protein Sequence and Structure (1972), National Biomedical Research Foundation, Washington, DC 89-99
    • (1972) Atlas of Protein Sequence and Structure , pp. 89-99
    • Dayhoff, M.O.1    Eck, R.V.2    Park, C.M.3
  • 6
    • 0000228203 scopus 로고
    • A model of evolutionary change in proteins
    • Dayhoff M.O. (Ed), National Biomedical Research Foundation, Washington, DC
    • Dayhoff M.O., Schwartz R.M., and Orcutt B.C. A model of evolutionary change in proteins. In: Dayhoff M.O. (Ed). Atlas of Protein Sequence and Structure (1978), National Biomedical Research Foundation, Washington, DC 345-352
    • (1978) Atlas of Protein Sequence and Structure , pp. 345-352
    • Dayhoff, M.O.1    Schwartz, R.M.2    Orcutt, B.C.3
  • 7
    • 0014214038 scopus 로고
    • Non-randomness of amino acid substitutions during the evolution of proteins
    • Epstein C.J. Non-randomness of amino acid substitutions during the evolution of proteins. Nature 215 (1967) 355-359
    • (1967) Nature , vol.215 , pp. 355-359
    • Epstein, C.J.1
  • 8
    • 0032893932 scopus 로고    scopus 로고
    • Preservation of duplicate genes by complementary, degenerative mutations
    • Force A., Lynch M., Pickett F.B., et al. Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151 (1999) 1531-1545
    • (1999) Genetics , vol.151 , pp. 1531-1545
    • Force, A.1    Lynch, M.2    Pickett, F.B.3
  • 9
    • 0028168856 scopus 로고
    • A codon-based model of nucleotide substitution for protein-coding DNA sequences
    • Goldman N., and Yang Z. A codon-based model of nucleotide substitution for protein-coding DNA sequences. Mol. Biol. Evol. 11 (1994) 725-736
    • (1994) Mol. Biol. Evol. , vol.11 , pp. 725-736
    • Goldman, N.1    Yang, Z.2
  • 10
    • 0016197604 scopus 로고
    • Amino acid difference formula to help explain protein evolution
    • Grantham R. Amino acid difference formula to help explain protein evolution. Science (1974) 185
    • (1974) Science , pp. 185
    • Grantham, R.1
  • 11
    • 0022180868 scopus 로고
    • Amino acid composition and the evolutionary rates of protein-coding genes
    • Graur D. Amino acid composition and the evolutionary rates of protein-coding genes. J. Mol. Evol. 22 (1985) 53-62
    • (1985) J. Mol. Evol. , vol.22 , pp. 53-62
    • Graur, D.1
  • 12
    • 0026327996 scopus 로고
    • A quantitative measure of error minimization in the genetic code
    • Haig D., and Hurst L.D. A quantitative measure of error minimization in the genetic code. J. Mol. Evol. 33 (1991) 412-417
    • (1991) J. Mol. Evol. , vol.33 , pp. 412-417
    • Haig, D.1    Hurst, L.D.2
  • 13
    • 0031875569 scopus 로고    scopus 로고
    • Evolutionary distances for protein-coding sequences: modeling site-specific residue frequencies
    • Halpern A.L., and Bruno W.J. Evolutionary distances for protein-coding sequences: modeling site-specific residue frequencies. Mol. Biol. Evol. 15 (1998) 910-917
    • (1998) Mol. Biol. Evol. , vol.15 , pp. 910-917
    • Halpern, A.L.1    Bruno, W.J.2
  • 14
    • 0022376704 scopus 로고
    • Dating of the human-ape splitting by a molecular clock of mitochondrial DNA
    • Hasegawa M., Kishino H., and Yano T. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol. 22 (1985) 160-174
    • (1985) J. Mol. Evol. , vol.22 , pp. 160-174
    • Hasegawa, M.1    Kishino, H.2    Yano, T.3
  • 15
    • 0028133496 scopus 로고
    • Converting trypsin to chymotrypsin: residue 172 is a substrate specificity determinant
    • Hedstrom L., Perona J.J., and Rutter W.J. Converting trypsin to chymotrypsin: residue 172 is a substrate specificity determinant. Biochemistry 33 (1994) 8757-8763
    • (1994) Biochemistry , vol.33 , pp. 8757-8763
    • Hedstrom, L.1    Perona, J.J.2    Rutter, W.J.3
  • 16
    • 0026458378 scopus 로고
    • Amino-acid substitution matrices from protein blocks
    • Henikoff S., and Henikoff J.G. Amino-acid substitution matrices from protein blocks. Proc. Natl. Acad. Sci. USA 89 (1992) 10915-10919
    • (1992) Proc. Natl. Acad. Sci. USA , vol.89 , pp. 10915-10919
    • Henikoff, S.1    Henikoff, J.G.2
  • 17
    • 0025147562 scopus 로고
    • Positive Darwinian selection promotes charge profile diversity in the antigen-binding cleft of class I major histocompatibility complex genes in mammals
    • Hughes A.L., Ota T., and Nei M. Positive Darwinian selection promotes charge profile diversity in the antigen-binding cleft of class I major histocompatibility complex genes in mammals. Mol. Biol. Evol. 7 (1990) 515-524
    • (1990) Mol. Biol. Evol. , vol.7 , pp. 515-524
    • Hughes, A.L.1    Ota, T.2    Nei, M.3
  • 20
    • 0032529584 scopus 로고    scopus 로고
    • Models of natural mutations including site heterogeneity
    • Koshi J.M., and Goldstein R.A. Models of natural mutations including site heterogeneity. Proteins 32 (1998) 289-295
    • (1998) Proteins , vol.32 , pp. 289-295
    • Koshi, J.M.1    Goldstein, R.A.2
  • 21
    • 0033026624 scopus 로고    scopus 로고
    • Using physical-chemistry-based substitution models in phylogenetic analyses of HIV-1 subtypes
    • Koshi J.M., Mindell D.P., and Goldstein R.A. Using physical-chemistry-based substitution models in phylogenetic analyses of HIV-1 subtypes. Mol. Biol. Evol. 16 (1999) 173-179
    • (1999) Mol. Biol. Evol. , vol.16 , pp. 173-179
    • Koshi, J.M.1    Mindell, D.P.2    Goldstein, R.A.3
  • 22
    • 0020475449 scopus 로고
    • A simple method for displaying the hydropathic character of a protein
    • Kyte J., and Dolittle R. A simple method for displaying the hydropathic character of a protein. J. Mol. Biol. 157 (1982) 105-132
    • (1982) J. Mol. Biol. , vol.157 , pp. 105-132
    • Kyte, J.1    Dolittle, R.2
  • 23
    • 0018953460 scopus 로고
    • Rate of gene silencing at duplicate loci: a theoretical study and interpretation of data from tetraploid fish
    • Li W.-H. Rate of gene silencing at duplicate loci: a theoretical study and interpretation of data from tetraploid fish. Genetics 95 (1980) 237-258
    • (1980) Genetics , vol.95 , pp. 237-258
    • Li, W.-H.1
  • 25
    • 0015505473 scopus 로고
    • Repeating sequences and gene duplication in proteins
    • McLachlan A.D. Repeating sequences and gene duplication in proteins. J. Mol. Biol. 64 (1972) 417-437
    • (1972) J. Mol. Biol. , vol.64 , pp. 417-437
    • McLachlan, A.D.1
  • 26
    • 0018415510 scopus 로고
    • Two types of amino acid substitution in protein evolution
    • Miyata T., Miyazawa S., and Yasunaga T. Two types of amino acid substitution in protein evolution. J. Mol. Evol. 12 (1979) 219-236
    • (1979) J. Mol. Evol. , vol.12 , pp. 219-236
    • Miyata, T.1    Miyazawa, S.2    Yasunaga, T.3
  • 27
    • 0028024626 scopus 로고
    • A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome
    • Muse S.V., and Gaut B.S. A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome. Mol. Biol. Evol. 11 (1994) 715-724
    • (1994) Mol. Biol. Evol. , vol.11 , pp. 715-724
    • Muse, S.V.1    Gaut, B.S.2
  • 28
    • 0031972161 scopus 로고    scopus 로고
    • Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene
    • Nielsen R., and Yang Z. Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics 148 (1998) 929-936
    • (1998) Genetics , vol.148 , pp. 929-936
    • Nielsen, R.1    Yang, Z.2
  • 29
    • 0034106726 scopus 로고    scopus 로고
    • Appropriate likelihood ratio tests and marginal distributions for evolutionary tree models with constraints on parameters
    • Ota R., Waddell P.J., Hasegawa M., Shimodaira H., and Kishino H. Appropriate likelihood ratio tests and marginal distributions for evolutionary tree models with constraints on parameters. Mol. Biol. Evol. 17 (2000) 798-803
    • (2000) Mol. Biol. Evol. , vol.17 , pp. 798-803
    • Ota, R.1    Waddell, P.J.2    Hasegawa, M.3    Shimodaira, H.4    Kishino, H.5
  • 30
    • 0035527377 scopus 로고    scopus 로고
    • Stochastic search strategy for estimation of maximum likelihood phylogenetic trees
    • Salter L.A., and Pearl D.K. Stochastic search strategy for estimation of maximum likelihood phylogenetic trees. Syst. Biol. 50 (2001) 7-17
    • (2001) Syst. Biol. , vol.50 , pp. 7-17
    • Salter, L.A.1    Pearl, D.K.2
  • 31
    • 84907319426 scopus 로고
    • Asymptotic properties of maximum likelihood estimators and likelihood ratio tests under nonstandard conditions
    • Self S.G., and Liang K.-Y. Asymptotic properties of maximum likelihood estimators and likelihood ratio tests under nonstandard conditions. J. Am. Stat. Assoc. 82 (1987) 605-610
    • (1987) J. Am. Stat. Assoc. , vol.82 , pp. 605-610
    • Self, S.G.1    Liang, K.-Y.2
  • 32
    • 0013965569 scopus 로고
    • Relations between chemical structure and biological activity
    • Sneath P.H.A. Relations between chemical structure and biological activity. J. Theor. Biol. 12 (1966) 157-195
    • (1966) J. Theor. Biol. , vol.12 , pp. 157-195
    • Sneath, P.H.A.1
  • 34
    • 0004248459 scopus 로고    scopus 로고
    • Sinauer, Sunderland, MA
    • Swofford D.L. PAUP* (2002), Sinauer, Sunderland, MA
    • (2002) PAUP*
    • Swofford, D.L.1
  • 35
    • 0027968068 scopus 로고
    • CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice
    • Thompson J.D., Higgins D.G., and Gibson T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22 (1994) 4673-4680
    • (1994) Nucleic Acids Res. , vol.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 36
    • 0029985399 scopus 로고    scopus 로고
    • Combining protein evolution and secondary structure
    • Thorne J.L., Goldman N., and Jones D.T. Combining protein evolution and secondary structure. Mol. Biol. Evol. 13 (1996) 666-673
    • (1996) Mol. Biol. Evol. , vol.13 , pp. 666-673
    • Thorne, J.L.1    Goldman, N.2    Jones, D.T.3
  • 37
    • 0034079112 scopus 로고    scopus 로고
    • Selective constraints, amino acid composition, and the rate of protein evolution
    • Tourasse N.J., and Li W.-H. Selective constraints, amino acid composition, and the rate of protein evolution. Mol. Biol. Evol. 17 (2000) 656-664
    • (2000) Mol. Biol. Evol. , vol.17 , pp. 656-664
    • Tourasse, N.J.1    Li, W.-H.2
  • 38
    • 0031766244 scopus 로고    scopus 로고
    • What amino acid properties affect protein evolution?
    • Xia X., and Li W.H. What amino acid properties affect protein evolution?. J. Mol. Evol. 47 (1998) 557-564
    • (1998) J. Mol. Evol. , vol.47 , pp. 557-564
    • Xia, X.1    Li, W.H.2
  • 39
    • 0027132974 scopus 로고
    • Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites
    • Yang Z. Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites. Mol. Biol. Evol. 10 (1993) 1396-1401
    • (1993) Mol. Biol. Evol. , vol.10 , pp. 1396-1401
    • Yang, Z.1
  • 40
    • 0028064845 scopus 로고
    • Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods
    • Yang Z. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. J. Mol. Evol. 39 (1994) 306-314
    • (1994) J. Mol. Evol. , vol.39 , pp. 306-314
    • Yang, Z.1
  • 41
    • 0033979433 scopus 로고    scopus 로고
    • Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models
    • Yang Z., and Nielsen R. Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Mol. Biol. Evol. 17 (2000) 32-43
    • (2000) Mol. Biol. Evol. , vol.17 , pp. 32-43
    • Yang, Z.1    Nielsen, R.2
  • 42
    • 0034097381 scopus 로고    scopus 로고
    • Codon-substitution models for heterogeneous selection pressure at amino acid sites
    • Yang Z., Nielsen R., Goldman N., and Pedersen A.-M.K. Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics 155 (2000) 431-449
    • (2000) Genetics , vol.155 , pp. 431-449
    • Yang, Z.1    Nielsen, R.2    Goldman, N.3    Pedersen, A.-M.K.4
  • 43
    • 0033800170 scopus 로고    scopus 로고
    • Maximum likelihood analysis of molecular adaptation in abalone sperm lysin reveals variable selective pressures among lineages and sites
    • Yang Z., Swanson W.J., and Vacquier V.D. Maximum likelihood analysis of molecular adaptation in abalone sperm lysin reveals variable selective pressures among lineages and sites. Mol. Biol. Evol. 17 (2000) 1446-1455
    • (2000) Mol. Biol. Evol. , vol.17 , pp. 1446-1455
    • Yang, Z.1    Swanson, W.J.2    Vacquier, V.D.3
  • 44
    • 0033921902 scopus 로고    scopus 로고
    • Rates of conservative and radical nonsynonymous nucleotide substitutions in mammalian nuclear genes
    • Zhang J. Rates of conservative and radical nonsynonymous nucleotide substitutions in mammalian nuclear genes. J. Mol. Evol. 50 (2000) 56-68
    • (2000) J. Mol. Evol. , vol.50 , pp. 56-68
    • Zhang, J.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.