Pair hidden Markov models on tree structures

Bioinformatics

Volumn 19, Issue SUPPL. 1, 2003, Pages

  Sakakibara, Yasubumi ^a  

^a KEIO UNIVERSITY   (Japan)

Author keywords

Hidden markov model; RNA; Secondary structure; Stochastic context free grammar; Structural alignment; Tree automaton

Indexed keywords

COMPARATIVE STUDY; CONFERENCE PAPER; MATHEMATICAL MODEL; PRIORITY JOURNAL; PROBABILITY; RNA SEQUENCE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; STRUCTURAL BIOINFORMATICS; THEORETICAL MODEL; ALGORITHM; ARTICLE; BIOLOGICAL MODEL; CHEMISTRY; CONFORMATION; EVALUATION; GENETICS; METHODOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; SEQUENCE HOMOLOGY; STATISTICAL MODEL; STATISTICS;

HAMMERHEAD RIBOZYME; RIBOZYME; RNA; TRANSFER RNA;

ALGORITHMS; BASE SEQUENCE; MARKOV CHAINS; MODELS, GENETIC; MODELS, STATISTICAL; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; RNA; RNA, CATALYTIC; RNA, TRANSFER; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, RNA; SEQUENCE HOMOLOGY, NUCLEIC ACID; STOCHASTIC PROCESSES;

EID: 4944232234     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btg1032     Document Type: Conference Paper

References (23)

1. Aho, A. and Ullman, J. (1972) The Theory of Parsing, Translation and Compiling, Vol. I: Parsing, Prentice Hall, Englewood Cliffs, NJ.
2. Durbin, R., Eddy, S., Krogh, A. and Mitchison, G. (1998) Biological Sequence Analysis. Cambridge University Press, Cambridge.
3. Eddy, S. and Durbin, R. (1994) RNA sequence analysis using covariance models. Nucleic Acids Res., 22, 2079-2088.
4. Eddy, S. (1998) Profile hidden Markov models. Bioinformatics, 14, 755-763.
5. Eddy, S. (2001) Noncoding RNA genes and the modern RNA world. Nat. Rev. Genet., 21, 919-929.
6. Griffiths-Jones, B., Bateman, A., Marshall, M., Khanna, A. and Eddy, S. (2003) Rfam: an RNA family database. Nucleic Acids Res., 31, 439-441. http://www.sanger.ac.uk/Software/Rfam/.
7. Gorodkin, J., Heyer, L. and Stormo, G. (1997) Finding the most significant common sequence and structure motifs in a set of RNA sequences. Nucleic Acids Res., 25, 3724-3732.
8. Holmes, I. and Rubin, G. (2002) Pairwise RNA structure comparison with stochastic context-free grammars. In Proceedings of 5th Pacific Symposium on Biocomputing. World Scientific Press, Singapore, pp. 163-174.
9. Jiang, T., Wang, L. and Zhang, K. (1995) Alignment of trees-an alternative to tree edit. Theor. Comp. Sci., 143, 137-148.
10. Jiang, T., Lin, G., Ma, B. and Zhang, K. (2002) A general edit distance between RNA structures. J. Comput. Biol., 9, 371-388.
11. Knudsen, B. and Hein, J. (1999) RNA secondary structure prediction using stochastic context-free grammars and evolutionary history. Bioinformatics, 15, 446-454.
12. Lari, K. and Young, S. (1990) The estimation of stochastic context-free grammars using the inside-outside algorithm. Computer Speech and Language, 4, 35-56.
13. Mathews, D. and Turner, D. (2002) Dynalign: an algorithm for finding the secondary structure common to two RNA sequences. J. Mol. Biol., 317, 191-203.
14. Pachter, L., Alexandersson, M. and Cawley, S. (2002) Applications of generalized pair hidden Markov models to alignment and gene finding problems. J. Comput. Biol., 9, 389-399.
15. Rivas, E. and Eddy, S. (2001) Noncoding RNA gene detection using comparative sequence analysis. BMC Bioinformatics, 2:8 (10 October 2001).
16. Sakakibara, Y., Brown, M., Hughey, R., Mian, I.S., Sjolander, K., Underwood, R.C. and Haussler, D. (1994) Stochastic context-free grammars for tRNA modeling. Nucleic Acids Res., 22, 5112-5120.
17. Sakakibara, Y. (1992) Efficient learning of context-free grammars from positive structural examples. Information and Computation, 97, 23-60.
18. Sankoff, D. (1985) Simultaneous solution of the RNA folding, alignment and protosequence problems. SIAM J. Appl. Math., 45, 810-825.
19. Schattner, P. (2002) Searching for RNA genes using base-composition statistics. Nucleic Acids Res., 30, 2076-2082.
20. Searls, D. and Murphy, K. (1995) Automata-theoretic models of mutation and alignment. Proceedings of 3rd International Conference on Intelligent Systems for Molecular Biology. AAAI Press, Menlo Park, CA, pp. 341-349.
21. Shapiro, B. and Zhang, K. (1990) Comparing multiple RNA secondary structures using tree comparisons. Comput. Appl. Biosci., 6, 309-318.
22. Steinberg, S., Misch, A. and Sprinzl, M. (1993) Compilation of tRNA sequences and sequences of tRNA genes. Nucleic Acids Res., 21, 3011-3015.
23. Thompson, J., Higgins, D. and Gibson, T. (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.