Pattern discovery in biosequences

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 1433, Issue , 1998, Pages 257-270

  Brāzma, Alvis ^a   Jonassen, Inge ^b   Vilo, Jaak ^c   Ukkonen, Esko ^c  

^a WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^b UNIVERSITY OF BERGEN   (Norway)

^c UNIVERSITY OF HELSINKI   (Finland)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING SITES; COMPUTATIONAL GRAMMARS;

BIOSEQUENCES; COMPUTATIONAL BIOLOGY; HYPOTHESIS SPACE; ITS APPLICATIONS; PATTERN DISCOVERY; RATING PATTERN; TRANSCRIPTION FACTOR BINDING SITES; YEAST GENOME;

TRANSCRIPTION;

EID: 81855197178     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/bfb0054081     Document Type: Conference Paper

References (40)

1. R. Aasland and F. A. Stewart. The chromo shadow domain, a second chromo domain in heterchromatin-binding protein 1, HP1. Nucleic Acids Research, 23: 3168-3173, 1995.
2. D. Angluin. Finding patterns common to a set of strings. J. of Comp. and Syst. Sei., 21: 46-62, 1980.
3. S. Arikawa, S. Miyano, A. Shinohara, S. Kuhara, Y. Mukouchi, and T. Shinohara. A Machine Discovery from Amino Acid Sequences by Decision Trees over Regular Patterns. New Generation Computing, pages 361-375, 1993.
4. A. Bairoch. PROSITE: a dictionary of sites and patterns in proteins. Nucleic Acids Research, 20: 2013-2018, 1992.
5. A. Brazma and K. Cerans. Noise-tolerant inductive synthesis of regular expressions from good examples. New Generation Computing, 15(1): 105-140, 1997.
6. A. Brazma, I. Jonassen, I.Eidhammer, and D. Gilbert. Approaches to automatic discovery of patterns in biosequences. Journal of Computational Biology, (2): (to appear), 1998.
7. A. Brazma, I. Jonassen, E. Ukkonen, and J. Vilo. Discovering patterns and subfamilies in biosequences. In Proc. of Fourth International Conference on Intelligent Systems for Molecular Biology, pages 34-43. AAAI Press, 1996.
8. A. Brazma, E. Ukkonen, and J. Vilo. Discovering unbounded unions of regular pattern languages from positive examples. In Proceedings of 7th Annual International Symposium on Algorithms and Computation (ISAAC-96), Lect. Notes in Computer Science, volume 1178, pages 95-104, December 1996.
9. V. Chvátal. A greedy heuristic for the set-covering problem. Math. Oper. Res., 4: 233-235, 1979.
10. J. L. DeRisi, V. R. Iyer, and P. O. Brown. Exploring the metabolic and genetic control of gene expression on a genomic scale. Science, 278: 680-686, 1997.
11. S. Dong and D. B. Searls. Gene structure prediction by linguistic methods. Genomics, 23: 540-551, 1992.
12. R. Giegerich and S. Kurtz. A comparison of imperative and purely functional suffix tree constructions. Science of Computer Programming, 25(2-3): 187-218, 1995.
13. A. Goffeau, B. G. Barrell, H. Bussey, R. W. Davis, B. Dujon, H. Feldmann, F. Gal-ibert, J. D. Hoheisel, C. Jacq, M. Johnston, E. J. Louis, H. W. Mewes, Y. Murakami, P. Philippsen, H. Tettelin, and S. G. Oliver. Life with 6000 genes. Science, 274: 546-567, 1996.
14. E. M. Gold. Language identification in the limit. Information and Control, 10: 447-474, 1967.
15. I. Jonassen. Efficient discovery of conserved patterns using a pattern graph. Comput. Appl. Biosci., 13: 509-522, 1997.
16. I. Jonassen, J. F. Collins, and D. G. Higgins. Finding flexible patterns in unaligned protein sequences. Prot. Sci., 4(8): 1587-1595, 1995.
17. A. Krogh, M. Brown, I. S. Mian, K. Sjoelander, and D. Haussler. Hidden Markov model in computational biology. Applications to protein modelling.Journal of Molecular Biology, 235: 1501-1531, 1994.
18. R. Lathrop, T. Webster, R. Smith, P. Winston, and T. Smith. Integrating AI with sequence analysis. In L. Hunter, editor, Artificial Intelligence and Molecular Biology, pages 211-258. AAAI Press/The MIT Press, 1993.
19. C. E. Lawrence, S. F. Altschul, M. S. Boguski, J. S. Liu, A. F. Neuwald, and J. C. Wootton. Detecting Subtle Sequence Signals: A Gibbs Sampling Strategy for Multiple Alignment. Science, 262: 208-214, Oct 1993.
20. M. Li and P. Vitanyi. An introduction to Kolmogorov complexity and its applications. Springer-Verlag, New York, 1993.
21. E. M. McCreight. A space-economical suffix tree construction algorithm. Journal of the ACM, 23: 262-272, 1976.
22. P. J. Mitchell and R. Tijan. Transcription regulation in mammalian cells by sequence-specific DNA binding proteins. Science, 245: 371-378, 1989.
23. A. F. Neuwald and P. Green. Detecting patterns in protein sequences. Journal of Molecular Biology, 239: 689-712, 1994.
24. R. Paro and D. H. Hogness. The polycomb protein shares a homologous domain with a heterochromatin-associated protein of drosophila. In Proc. Ntatl. Acad. Sci. USA, pages 263-267, Jan 1991.
25. G. Ramsay. DNA chips: State-of-the-art. Nature Biotechnology, 16: 40-44, 1998.
26. J. Rissanen. Modeling by the shortest data description. Automatica-J.IFAC, 14: 465-471, 1978.
27. M-F. Sagot, A. Viari, and H. Soldano. Multiple sequence comparison: a peptide matching approach. In Z. Galil and E. Ukkonen, editors, Proc. of 6th Annual Symposium on Combinatorial Pattern Matching, Lecture Notes in Computer Science 937, pages 366-385. Springer, July 1995.
28. R. F. Sewell and R. Durbin. Method for calculation of probability of matching a bounded regular expression in a random data string. Journal of Computational Biology, 2: 25-31, 1995.
29. T. Shinohara. Polynomial time inference of extended regular pattern languages. Lect. Notes in Computer Science, 147: 115-127, 1983.
30. H. O. Smith, T. M. Annau, and S. Chandrasegaran. Finding sequence motifs in groups of functionally related proteins. In Proc. Natl. Acad. Sci. USA, pages 826-830, Jan 1990.
31. R. F. Smith and T. F. Smith. Automatic generation of primary sequence patterns from sets of related protein sequences. In Proc. Natl. Acad. Sci. USA, pages 118-122, Jan 1990.
32. R. Staden. Methods for calculating the probabilities of finding patterns in sequences. CABIOS, 5: 89-96, 1989.
33. R. Staden. Methods for discovering novel motifs in nucleic acid sequences. CABIOS, 5(4): 293-298, 1989.
34. T. G. Turi and J. C. Loper. Multiple regulatory elements control expression of the gene encoding the Saccharomyces cerevisiae cytochrome P450, lanosterol 14 alpha-demethylase (ERG11). Journal of Biological Chemistry, 267: 2046-2056, 1992.
35. E. Ukkonen. On-line construction of suffix trees. Algorithmica, 14: 249-260, 1995.
36. J. Vilo. Discovering frequent patterns from strings. Technical Report C-1998-9, Department of Computer Science, University of Helsinki, P. O. Bo 26, FIN-00014, University of Helsinki, May 1998.
37. M. Vingron and P. Argos. Motif Recognition and Alignment for Many Sequences by Comparison of Dot-matrices. Journal of Molecular Biology, 218: 33-43, 1991.
38. L. Wang and T. Jiang. One the complexity of multiple sequence alignment. Journal of Computational Biology, 1(4): 337-348, 1994.
39. M. S. Waterman, R. Arratia, and D. J. Galas. Pattern Recognition in Several Sequences: Consensus and Alignment. Bulletin of Mathematical Biology, 46(4): 515-527, 1984.
40. E. Wingender, P. Dietze, H. Karas, and R. Knuppel. TRANSFAC: a database of transcriptional factors and their DNA binding sites. Nucleic Acids Research, 24: 238-241, 1996.