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Volumn 33, Issue 4, 2006, Pages 651-671

Parameter estimation in pair-hidden Markov models

Author keywords

Pair hidden Markov models; Score parameters estimation; Sequence alignment; TKF evolution model

Indexed keywords


EID: 33750994900     PISSN: 03036898     EISSN: 14679469     Source Type: Journal    
DOI: 10.1111/j.1467-9469.2006.00513.x     Document Type: Article
Times cited : (8)

References (24)
  • 2
    • 0000342467 scopus 로고
    • Statistical inference for probabilistic functions of finite state Markov chains
    • Baum, L. & Petrie, T. (1966). Statistical inference for probabilistic functions of finite state Markov chains. Ann. Math. Statis. 37, 1554-1563.
    • (1966) Ann. Math. Statis. , vol.37 , pp. 1554-1563
    • Baum, L.1    Petrie, T.2
  • 3
    • 0022474446 scopus 로고
    • Maximum likelihood alignment of DNA sequences
    • Bishop, M. & Thompson, E. (1986). Maximum likelihood alignment of DNA sequences. J. Mol. Biol. 190, 159-165.
    • (1986) J. Mol. Biol. , vol.190 , pp. 159-165
    • Bishop, M.1    Thompson, E.2
  • 4
    • 0036648783 scopus 로고    scopus 로고
    • Convergence of the maximum a posteriori path estimator in hidden Markov models
    • Caliebe, A. & Rösler, U. (2002). Convergence of the maximum a posteriori path estimator in hidden Markov models. IEEE Trans. Inf. Theory 48, 1750-1758.
    • (2002) IEEE Trans. Inf. Theory , vol.48 , pp. 1750-1758
    • Caliebe, A.1    Rösler, U.2
  • 5
    • 84889281816 scopus 로고
    • Wiley Series in Telecommunications. John Wiley & Sons, New York, NY, USA
    • Cover, T. M. & Thomas, J. A. (1991). Elements of information theory. Wiley Series in Telecommunications. John Wiley & Sons, New York, NY, USA.
    • (1991) Elements of Information Theory
    • Cover, T.M.1    Thomas, J.A.2
  • 6
    • 0003966087 scopus 로고
    • Information theory. Coding theorems for discrete memoryless systems
    • Academic Press, New York
    • Csiszár, I. & Körner, J. (1981). Information theory. Coding theorems for discrete memoryless systems. Probability and mathematical statistics. Academic Press, New York.
    • (1981) Probability and Mathematical Statistics
    • Csiszár, I.1    Körner, J.2
  • 7
    • 0035246117 scopus 로고    scopus 로고
    • Reliable communication over channels with insertions, deletions, and substitutions
    • Davey, M. C. & MacKay, D. J. (2001). Reliable communication over channels with insertions, deletions, and substitutions. IEEE Trans. Inf. Theory 47, 687-698.
    • (2001) IEEE Trans. Inf. Theory , vol.47 , pp. 687-698
    • Davey, M.C.1    MacKay, D.J.2
  • 9
    • 0034623015 scopus 로고    scopus 로고
    • Statistical alignment: Computational properties, homology testing and goodness-of-fit
    • Hein, J., Wiuf, C., Knudsen, B., Moller, M. & Wibling, G. (2000). Statistical alignment: computational properties, homology testing and goodness-of-fit. J. Mol. Biol. 302, 265-279.
    • (2000) J. Mol. Biol. , vol.302 , pp. 265-279
    • Hein, J.1    Wiuf, C.2    Knudsen, B.3    Moller, M.4    Wibling, G.5
  • 10
    • 15944375449 scopus 로고    scopus 로고
    • Applications of hidden Markov models for characterization of homologous DNA sequences with a common gene
    • Hobolth, A. & Jensen, J. L. (2005). Applications of hidden Markov models for characterization of homologous DNA sequences with a common gene. J. Comput. Biol. 12, 186-203.
    • (2005) J. Comput. Biol. , vol.12 , pp. 186-203
    • Hobolth, A.1    Jensen, J.L.2
  • 11
    • 19544384204 scopus 로고    scopus 로고
    • Using evolutionary expectation maximization to estimate indel rates
    • Holmes, I. (2005). Using evolutionary expectation maximization to estimate indel rates. Bioinformatics 21, 2294-2300.
    • (2005) Bioinformatics , vol.21 , pp. 2294-2300
    • Holmes, I.1
  • 12
    • 0003789496 scopus 로고
    • Statistical estimation. Asymptotic theory
    • Springer-Verlag, New York
    • Ibragimov, I. A. & Has'minskii, R. Z. (1981). Statistical estimation. Asymptotic theory. Applications of mathematics, Vol. 16. Springer-Verlag, New York.
    • (1981) Applications of Mathematics , vol.16
    • Ibragimov, I.A.1    Has'Minskii, R.Z.2
  • 14
    • 0141869092 scopus 로고    scopus 로고
    • Sequence alignments and pair hidden Markov models using evolutionary history
    • Knudsen, B. & Miyamoto, M. M. (2003). Sequence alignments and pair hidden Markov models using evolutionary history. J. Mol. Biol. 333, 453-460.
    • (2003) J. Mol. Biol. , vol.333 , pp. 453-460
    • Knudsen, B.1    Miyamoto, M.M.2
  • 15
    • 0001572082 scopus 로고
    • Maximum-likelihood estimation for hidden Markov models
    • Leroux, B. G. (1992). Maximum-likelihood estimation for hidden Markov models. Stochastic Process. Appl. 40, 127-143.
    • (1992) Stochastic Process. Appl. , vol.40 , pp. 127-143
    • Leroux, B.G.1
  • 16
    • 0035089745 scopus 로고    scopus 로고
    • Efficient reconstruction of sequences
    • Levenshtein, V. I. (2001). Efficient reconstruction of sequences. IEEE Trans. Inf. Theory 47, 2-22.
    • (2001) IEEE Trans. Inf. Theory , vol.47 , pp. 2-22
    • Levenshtein, V.I.1
  • 17
    • 0037339432 scopus 로고    scopus 로고
    • Statistical alignment based on fragment insertion and deletion models
    • Metzler, D. (2003). Statistical alignment based on fragment insertion and deletion models. Bioinformatics 19, 490-499.
    • (2003) Bioinformatics , vol.19 , pp. 490-499
    • Metzler, D.1
  • 18
    • 0036772510 scopus 로고    scopus 로고
    • Comparative ab initio prediction of gene structures using pair HMMs
    • Meyer, I. M. & Durbin, R. (2002). Comparative ab initio prediction of gene structures using pair HMMs. Bioinformatics 18, 1309-1318.
    • (2002) Bioinformatics , vol.18 , pp. 1309-1318
    • Meyer, I.M.1    Durbin, R.2
  • 19
    • 1542510093 scopus 로고    scopus 로고
    • A "long indel" model for evolutionary sequence alignment
    • Miklos, I., Lunter, G. A. & Holmes, I. (2004). A "long indel" model for evolutionary sequence alignment. Mol. Biol. Evol. 21, 529-540.
    • (2004) Mol. Biol. Evol. , vol.21 , pp. 529-540
    • Miklos, I.1    Lunter, G.A.2    Holmes, I.3
  • 20
    • 0014757386 scopus 로고
    • A general method applicable to the search for similarities in the amino acid sequence of two proteins
    • Needleman, S. & Wunsch, C. (1970). A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol. 48, 443-453.
    • (1970) J. Mol. Biol. , vol.48 , pp. 443-453
    • Needleman, S.1    Wunsch, C.2
  • 21
    • 0036112213 scopus 로고    scopus 로고
    • Applications of generalized pair hidden Markov models to alignment and gene finding problems
    • Pachter, L., Alexandersson, M. & Cawley, S. (2002). Applications of generalized pair hidden Markov models to alignment and gene finding problems. J. Comput. Biol. 9, 389-399.
    • (2002) J. Comput. Biol. , vol.9 , pp. 389-399
    • Pachter, L.1    Alexandersson, M.2    Cawley, S.3
  • 22
    • 33751008827 scopus 로고
    • On mixing and the Zero-One law
    • Sucheston, L. (1963). On mixing and the Zero-One law. J. Math. Anal. Appl. 6, 447-456.
    • (1963) J. Math. Anal. Appl. , vol.6 , pp. 447-456
    • Sucheston, L.1
  • 23
    • 0026079507 scopus 로고
    • An evolutionary model for maximum likelihood alignment of DNA sequences
    • Thorne, J., 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.1    Kishino, H.2    Felsenstein, J.3
  • 24
    • 0026528734 scopus 로고
    • Inching toward reality: An improved likelihood model of sequence evolution
    • Thorne, J., Kishino, H. & Felsenstein, J. (1992). Inching toward reality: an improved likelihood model of sequence evolution. J. Mol. Evol. 34, 3-16.
    • (1992) J. Mol. Evol. , vol.34 , pp. 3-16
    • Thorne, J.1    Kishino, H.2    Felsenstein, J.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.