Using guide trees to construct multiple-sequence evolutionary HMMs

Bioinformatics

Volumn 19, Issue SUPPL. 1, 2003, Pages

  Holmes, I ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; CONFERENCE PAPER; PHYLOGENETIC TREE; PRIORITY JOURNAL; PROBABILITY; SEQUENCE ALIGNMENT; STATISTICAL ANALYSIS; ARTICLE; BIOLOGICAL MODEL; CLUSTER ANALYSIS; COMPARATIVE STUDY; COMPUTER PROGRAM; DNA SEQUENCE; EVALUATION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; METHODOLOGY; MOLECULAR EVOLUTION; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; STATISTICAL MODEL; VALIDATION STUDY;

ALGORITHMS; CLUSTER ANALYSIS; EVOLUTION, MOLECULAR; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; MARKOV CHAINS; MODELS, GENETIC; MODELS, STATISTICAL; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SEQUENCE ANALYSIS, PROTEIN; SEQUENCE HOMOLOGY; SOFTWARE;

EID: 0345457233     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btg1019     Document Type: Conference Paper

References (8)

1. Durbin, R., Eddy, S., Krogh, A. and Mitchison, G. (1998) Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids. Cambridge University Press, Cambridge, UK.
2. Eskin, E., Grundy, W.N. and Singer, Y. (2000) Protein family classification using sparse Markov transducers. In Bourne, P., Gribskov, M., Altman, R., Jensen, N., Hope, D., Lengauer, T., Mitchell, J., Scheeff, E., Smith, C., Strande, S. and Weissig, H. (eds), Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology. AAAI Press, Menlo Park, CA, pp. 134-135.
3. Friedman, N., Ninio, M., Pe'er, I. and Pupko, T. (2001) A structural EM algorithm for phylogenetic inference. In Lengauer, T., Sankoff, D., Istrail, S., Pevzner, P. and Waterman, M. (eds), Proceedings of the Fifth Annual International Conference on Computational Biology. Association for Computing Machinery, New York.
4. Hein, J., Wiuf, C., Knudsen, B., Moller, M.B. and Wibling, G. (2000) Statistical alignment: computational properties, homology testing and goodness-of-fit. J. Mol. Biol., 302, 265-279.
5. Holmes, I. and Bruno, W.J. (2001) Evolutionary HMMs: a Bayesian approach to multiple alignment. Bioinformatics, 17(9), 803-820.
6. Holmes, I. and Rubin, G.M. (2002) An expectation maximization algorithm for training hidden substitution models. J. Mol. Biol., 317(5), 757-768.
7. Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673-4680.
8. Thorne, J.L., Kishino, H. and Felsenstein, J. (1991) An evolutionary model for maximum likelihood alignment of DNA sequences. J. Mol. Evol., 33, 114-124.