An efficient algorithm for the extended (l,d)-motif problem with unknown number of binding sites

Proceedings - BIBE 2005: 5th IEEE Symposium on Bioinformatics and Bioengineering

Volumn 2005, Issue , 2005, Pages 11-18

  Leung, Henry C M ^a   Chin, Francis Y L ^a  

^a UNIVERSITY OF HONG KONG   (Hong Kong)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING SITES; MOTIF LENGTH;

COMPUTATIONAL METHODS; COMPUTER SOFTWARE; DNA SEQUENCES; MOLECULAR ORIENTATION; PATTERN RECOGNITION; PROBLEM SOLVING;

ALGORITHMS;

EID: 33751167615     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/BIBE.2005.12     Document Type: Conference Paper

References (25)

1. T. Bailey and C. Elkan. Unsupervised learning of multiple motifs in biopolymers using expectation maximization. Machine Learning, 21, 1995, pp 51-80.
2. A. Brazma, I. Jonassen, I. Eidhammer and D. Gilbert. Approaches to the automatic discovery of patterns in biosequences. Journal of Computational Biology, 5, 1998, pp 279-305.
3. J. Buhler and M. Tompa. Finding motifs using random projections. In Proc. of RECOMB01, 2001, pp 69-76.
4. F.Y.L. Chin and H.C.M. Leung. Voting algorithm for discovering long motifs. In Proc. of Asia-Pacific Bioinforinatics Conference, 2005, pp 261-272.
5. F.Y.L. Chin, H.C.M. Leung, S.M. Yiu, T.W. Lam, R. Rosenfeld, W.W. Tsang, D.K. Smith and T. Jiang. Finding motifs for insufficient number of sequences with strong binding to transcription factor. In Proc. of RECOMB04, 2004, pp 125-132.
6. C. Lawrence, S. Altschul, M. Boguski, J. Liu, A. Neuwald and J. Wootton. Detecting subtule sequence signals: a Gibbs sampling strategy for multiple alignment. Science, 262, 1993, pp 208-214.
7. C. Lawrence and A. Reilly. An expectation maximization (em) algorithm for the identification and characterization of common sites in unaligned biopolymer sequences. Proteins: Structure, Function and Genetics, 7, 1990, pp 41-51.
8. H.C.M. Leung and F.Y.L. Chin. Algorithms for Challenging Motif Problem. Journal of Bioinformatics and Computational Biology (JBCE), 2005 (to appear)
9. H.C.M. Leung and F.Y.L. Chin. Finding Exact Optimal Motif in Matrix Representation by Partitioning. In Proc. of European Conference on Computational Biology, 2005 (to appear).
10. H.C.M. Leung and F.Y.L. Chin. Generalized Planted (l,d)-Motif Problem with Negative Set. In Proc. of Workshop on Algorithms in Bioinformatics (WABI), 2005. (will appear)
11. H.C.M. Leung, F.Y.L. Chin, S.M. Yiu, R. Rosenfeld and W.W. Tsang. Finding motifs with insufficient number of strong binding sites. Journal of Computational Biology, 2005 (to appear).
12. M. Li, B. Ma, and L. Wang. Finding similar regions in many strings. Journal of Computer and System Sciences, 65, 2002, pp 73-96.
13. S. Liang. cWINNOWER Algorithm for Finding Fuzzy DNA Motifs. In Proc. of Computer Society Bioinformatics Conference, 2003, pp 260-265.
14. K. Makino and T. Uno. New algorithms for enumerating all maximal cliques. In Proc. of Scandinavian Workshop on Algorithm Theory, 2004, pp 260-272.
15. H. Ono and Y.K. Ng. Best Fitting-Length Substring Patterns for a Set of Strings. COCOON, 2005.
16. G. Pesole, N. Prunella, S. Liuni, M. Attimonelli, and C. Saccone. Wordup: an efficient algorithm for discovering statistically significant patterns in dna sequences. Nucl. Acids Res., 20(11), 1992, pp 2871-2875.
17. P. Pevzner and S.H. Sze. Combinatorial approaches to finding subtle signals in dna sequences. In Proc. of the Eighth International Conference on Intelligent Systems for Molecular Biology, 2000, pp 269-278.
18. A. Price, S. Ramabhadran and P.A. Pevzner. Finding subtle motifs by branching from sample strings. Bioinformatics, 1, 2003, pp 1-7.
19. S. Rajasekaran, S. Balla and C.H. Huang. Exact algorithm for planted motif challenge problems. In Proc. of Asia-Pacific Bioinformatics Conference, 2005, pp 249-259.
20. I. Rigoutsos and A. Floratos. Combinatorial pattern discovery in biological sequences: The TEIRESIAS algorithm. Bioinformatics, 14, 1998, pp 55-67.
21. M.F. Sagot. Spelling approximate repeated or common motifs using a suffix tree. Latin'98: Theoretical informatics, volume 1380 of Lecture Notes in Computer Science, C.L. Lucchesi and A.V. Moura editors, 1998, pp 111-127.
22. M.P. Styczynski, K.L. Jensen, I. Rigoutsos and G.N. Stephanopoulos. An extension and novel solution to the (l,d)-motif challenge problem. Genome Informatics, 15, 2004, pp 63-71.
23. M. Tompa. An exact method for finding short motifs in sequences with application to the ribosome binding site problem. In Proc. of the 7th International Conference on Intelligent Systems for Molecular Biology, 1999, pp 262-271.
24. F. Wolfertsteeter, K. Frech, G. Herrmann, and T. Wernet. Identification of functional elements in unaligned nucleic acid sequences by a novel tuple search algorithm. Computer Applications in Bio-sciences, 12(1), 1996, pp 71-80.
25. J. Zhu and M. Zhang. SCPD: a promoter database of the yeast Saccha-romyces cerevisiae. Bioinformatics, 15, 1999, pp 563-577. http://cgsigma.cshl.org/jian/