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Volumn 62, Issue 6, 2006, Pages 663-673

Efficient methods for estimating amino acid replacement rates

Author keywords

Amino acid replacement; General time reversible model; Markov model; Parameter estimation; Protein evolution

Indexed keywords

AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ANALYTIC METHOD; ARTICLE; INFORMATION PROCESSING; INTERMETHOD COMPARISON; METHODOLOGY; PHYLOGENY; PROTEIN DOMAIN;

EID: 33744907021     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-004-0113-9     Document Type: Article
Times cited : (15)

References (40)
  • 1
    • 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
    • (1996) J Mol Evol , vol.42 , pp. 459-468
    • Adachi, J.1    Hasegawa, M.2
  • 2
    • 0029999739 scopus 로고    scopus 로고
    • A Bayesian evolutionary distance for parametrically aligned sequences
    • Agarwal P, States DJ (1996) A Bayesian evolutionary distance for parametrically aligned sequences. J Comput Biol 3:1-17
    • (1996) J Comput Biol , vol.3 , pp. 1-17
    • Agarwal, P.1    States, D.J.2
  • 4
    • 0031453046 scopus 로고    scopus 로고
    • Estimation of reversible substitution matrices from multiple pairs of sequences
    • Arvestad L, Bruno WJ (1997) Estimation of reversible substitution matrices from multiple pairs of sequences. J Mol Evol 45:696-703
    • (1997) J Mol Evol , vol.45 , pp. 696-703
    • Arvestad, L.1    Bruno, W.J.2
  • 6
    • 0022358402 scopus 로고
    • Evolutionary trees from nucleic acid and protein sequences
    • Bishop M, Friday A (1985) Evolutionary trees from nucleic acid and protein sequences. Proc R Soc Lond B 226:272-302
    • (1985) Proc R Soc Lond B , vol.226 , pp. 272-302
    • Bishop, M.1    Friday, A.2
  • 7
    • 0028172520 scopus 로고
    • Phylogenetic relationships among eutharian orders estimated from inferred sequences of mitochondrial proteins: Instability of a tree based on a single gene
    • Cao Y, Adachi J, Janke A, Pääbo S, Hasegawa M (1994) Phylogenetic relationships among eutharian orders estimated from inferred sequences of mitochondrial proteins: Instability of a tree based on a single gene. J Mol Evol 39:519-527
    • (1994) J Mol Evol , vol.39 , pp. 519-527
    • Cao, Y.1    Adachi, J.2    Janke, A.3    Pääbo, S.4    Hasegawa, M.5
  • 8
    • 0002929101 scopus 로고
    • A model of evolutionary change in proteins
    • Dayhoff MO (ed) National Biomedical Research Foundation, Washington, D.C.
    • Dayhoff MO, Eck RV, Park CM (1972) A model of evolutionary change in proteins. In: Dayhoff MO (ed) Atlas of protein sequence and structure, National Biomedical Research Foundation, Washington, D.C., vol 5, pp 89-99
    • (1972) Atlas of Protein Sequence and Structure , vol.5 , pp. 89-99
    • Dayhoff, M.O.1    Eck, R.V.2    Park, C.M.3
  • 11
    • 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
  • 13
    • 0036856275 scopus 로고    scopus 로고
    • A novel use of equilibrium frequencies in models of sequence evolution
    • Goldman N, Whelan S (2002) A novel use of equilibrium frequencies in models of sequence evolution. Mol Biol Evol 19:1821-1831
    • (2002) Mol Biol Evol , vol.19 , pp. 1821-1831
    • Goldman, N.1    Whelan, S.2
  • 14
    • 0030601801 scopus 로고    scopus 로고
    • Using evolutionary trees in protein secondary structure prediction and other comparative sequence analyses
    • Goldman N, Thorne JL, Jones DT (1996) Using evolutionary trees in protein secondary structure prediction and other comparative sequence analyses. J Mol Biol 263:196-208
    • (1996) J Mol Biol , vol.263 , pp. 196-208
    • Goldman, N.1    Thorne, J.L.2    Jones, D.T.3
  • 16
    • 0026656815 scopus 로고
    • Exhaustive matching of the entire protein sequence database
    • Gonnet GH, Cohen M, Benner S (1992) Exhaustive matching of the entire protein sequence database. Science 256:1443-1445
    • (1992) Science , vol.256 , pp. 1443-1445
    • Gonnet, G.H.1    Cohen, M.2    Benner, S.3
  • 18
    • 0026458378 scopus 로고
    • Amino acid substitution matrices from protein blocks
    • USA
    • 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 , vol.89 , pp. 10915-10919
    • Henikoff, S.1    Henikoff, J.G.2
  • 19
    • 0036298990 scopus 로고    scopus 로고
    • An expectation maximization algorithm for training hidden substitution models
    • Holmes I, Rubin GM (2002) An expectation maximization algorithm for training hidden substitution models. J Mol Biol 317:753-764
    • (2002) J Mol Biol , vol.317 , pp. 753-764
    • Holmes, I.1    Rubin, G.M.2
  • 20
    • 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. Comput Appl Biosci 8:275-282
    • (1992) Comput Appl Biosci , vol.8 , pp. 275-282
    • Jones, D.T.1    Taylor, W.R.2    Thornton, J.M.3
  • 23
    • 0028808763 scopus 로고
    • Context-dependent optimal substitution matrices
    • Koshi JM, Goldstein RA (1995) Context-dependent optimal substitution matrices. Protein Eng 8:641-645
    • (1995) Protein Eng , vol.8 , pp. 641-645
    • Koshi, J.M.1    Goldstein, R.A.2
  • 24
    • 0029881442 scopus 로고    scopus 로고
    • Probabilistic reconstruction of ancestral protein sequences
    • Koshi JM, Goldstein RA (1996) Probabilistic reconstruction of ancestral protein sequences. J Mol Evol 42:313-320
    • (1996) J Mol Evol , vol.42 , pp. 313-320
    • Koshi, J.M.1    Goldstein, R.A.2
  • 25
    • 0021277009 scopus 로고
    • A new method for calculating evolutionary substitution rates
    • Lanave C, Preparata G, Saccone C, Serio G (1984) A new method for calculating evolutionary substitution rates. J Mol Evol 20:86-93
    • (1984) J Mol Evol , vol.20 , pp. 86-93
    • Lanave, C.1    Preparata, G.2    Saccone, C.3    Serio, G.4
  • 26
    • 0036213764 scopus 로고    scopus 로고
    • Modeling mitochondrial protein evolution using structural information
    • Liò P, Goldman N (2002) Modeling mitochondrial protein evolution using structural information. J Mol Evol 54:519-529
    • (2002) J Mol Evol , vol.54 , pp. 519-529
    • Liò, P.1    Goldman, N.2
  • 27
    • 0031788749 scopus 로고    scopus 로고
    • PASSML: Combining evolutionary inference and protein secondary structure prediction
    • Liò P, Goldman N, Thorne JL, Jones DT (1998) PASSML: combining evolutionary inference and protein secondary structure prediction. Bioinformatics 14:726-733
    • (1998) Bioinformatics , vol.14 , pp. 726-733
    • Liò, P.1    Goldman, N.2    Thorne, J.L.3    Jones, D.T.4
  • 28
    • 0034922289 scopus 로고    scopus 로고
    • Modeling amino acid replacement
    • Müller T, Vingron M (2000) Modeling amino acid replacement. J Comput Biol 7:761-776
    • (2000) J Comput Biol , vol.7 , pp. 761-776
    • Müller, T.1    Vingron, M.2
  • 29
    • 0036134748 scopus 로고    scopus 로고
    • Estimating amino acid substitution models: A comparison of Dayhoff's estimator, the resolvent approach and a maximum likelihood method
    • Müller T, Spang R, Vingron M (2002) Estimating amino acid substitution models: a comparison of Dayhoff's estimator, the resolvent approach and a maximum likelihood method. Mol Biol Evol 19:8-13
    • (2002) Mol Biol Evol , vol.19 , pp. 8-13
    • Müller, T.1    Spang, R.2    Vingron, M.3
  • 30
    • 0023989064 scopus 로고
    • Improved tools for biological sequence comparison
    • USA
    • Pearson W, Lipman DJ (1988) Improved tools for biological sequence comparison. Proc Natl Acad Sci USA 85:2444-2448
    • (1988) Proc Natl Acad Sci , vol.85 , pp. 2444-2448
    • Pearson, W.1    Lipman, D.J.2
  • 31
    • 0033582946 scopus 로고    scopus 로고
    • Coevolving protein residues: Maximum likelihood identification and relationship to structure
    • Pollock D, Taylor W, Goldman N (1999) Coevolving protein residues: maximum likelihood identification and relationship to structure. J Mol Biol 287:187-198
    • (1999) J Mol Biol , vol.287 , pp. 187-198
    • Pollock, D.1    Taylor, W.2    Goldman, N.3
  • 32
    • 0035350525 scopus 로고    scopus 로고
    • A test of amino acid reversibility
    • Smith NG, Eyre-Walker A (2001) A test of amino acid reversibility. J Mol Evol 52:467-469
    • (2001) J Mol Evol , vol.52 , pp. 467-469
    • Smith, N.G.1    Eyre-Walker, A.2
  • 33
    • 0033043696 scopus 로고    scopus 로고
    • Is there a phylogenetic signal in prokaryote proteins?
    • Teichmann S, Mitchison G (1999) Is there a phylogenetic signal in prokaryote proteins? J Mol Evol 49:98-107
    • (1999) J Mol Evol , vol.49 , pp. 98-107
    • Teichmann, S.1    Mitchison, G.2
  • 34
    • 0033674329 scopus 로고    scopus 로고
    • Models of protein sequence evolution and their applications
    • Thorne JL (2000) Models of protein sequence evolution and their applications. Curr Opin Genet Dev 10:602-605
    • (2000) Curr Opin Genet Dev , vol.10 , pp. 602-605
    • Thorne, J.L.1
  • 35
    • 0742286995 scopus 로고    scopus 로고
    • A transition probability model for amino acid substitutions from blocks
    • Veerassamy S, Smith A, Tillier ER (2003) A transition probability model for amino acid substitutions from blocks. J Comput Biol 10:997-1010
    • (2003) J Comput Biol , vol.10 , pp. 997-1010
    • Veerassamy, S.1    Smith, A.2    Tillier, E.R.3
  • 36
    • 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) A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Mol Biol Evol 18:691-699
    • (2001) Mol Biol Evol , vol.18 , pp. 691-699
    • Whelan, S.1    Goldman, N.2
  • 37
    • 0041385962 scopus 로고    scopus 로고
    • PANDIT: A database of protein and associated nucleotide domains with inferred trees
    • Whelan S, de Bakker PI, Goldman N (2003) PANDIT: a database of protein and associated nucleotide domains with inferred trees. Bioinformatics 19:1556-1563
    • (2003) Bioinformatics , vol.19 , pp. 1556-1563
    • Whelan, S.1    De Bakker, P.I.2    Goldman, N.3
  • 38
    • 0030683599 scopus 로고    scopus 로고
    • PAML: A program package for phylogenetic analysis by maximum likelihood
    • Yang Z (1997) PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci 13:555-556
    • (1997) Comput Appl Biosci , vol.13 , pp. 555-556
    • Yang, Z.1
  • 39
    • 0028820333 scopus 로고
    • A new method of inference of ancestral nucleotide and amino acid sequences
    • Yang Z, Kumar S, Nei M (1995) A new method of inference of ancestral nucleotide and amino acid sequences. Genetics 141:1641-1650
    • (1995) Genetics , vol.141 , pp. 1641-1650
    • Yang, Z.1    Kumar, S.2    Nei, M.3
  • 40
    • 0346734129 scopus 로고    scopus 로고
    • The compositional adjustment of amino acid substitution matrices
    • USA
    • Yu Y, Wootton J, Altschul S (2003) The compositional adjustment of amino acid substitution matrices. Proc Natl Acad Sci USA 100:15688-15693
    • (2003) Proc Natl Acad Sci , vol.100 , pp. 15688-15693
    • Yu, Y.1    Wootton, J.2    Altschul, S.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.