From profiles to patterns and back again: A branch and bound algorithm for finding near optimal motif profiles

Proceedings of the Annual International Conference on Computational Molecular Biology, RECOMB

Volumn 8, Issue , 2004, Pages 115-124

  Eskin, Eleazar ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Motif finding; Patterns; Profiles; Transcription factor binding sites

Indexed keywords

COMPUTATIONAL BIOLOGY; MOTIF-FINDING; MULTIPLE SEQUENCING; PATTERNS; POSITION SPECIFIC SCORING MATRIX (PSSM); PROFILES; TRANSCRIPTION FACTOR BINDING SITES;

GENE TRANSFER; GENES; GENETIC ALGORITHMS; MOLECULAR BIOLOGY; OPTIMIZATION; PATTERN MATCHING;

GENETIC ENGINEERING;

EID: 2442591721     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (20)

1. T. L. Bailey and C. Elkan. Unsupervised learning of multiple motifs in biopolymers using expectation maximization. Machine Learning, 21:51, 1995.
2. Yoseph Barash, Gill Bejerano, and Nir Friedman. A simple hyper-geometric approach for discovering putative transcription factor binding sites. In Proceedings of WABI, 2001.
3. O.G. Berg and P. H. von Hippel. Selection of DNA binding sites by regulatory proteins. Trends Biochem Sci., 13:207-211, Jun 1998.
4. J. Buhler and M. Tompa. Finding motifs using random projections. In Proceedings of the Fifth Annual International Conference on Computational Molecular Biology (RECOMB01), pages 69-76, 2001.
5. A. P. Dempster, N. Laird, and D. Rubin. Maximum likelihood for incomplete data via the EM algorithm. Journal of the Royal Statistical Society, ser. B, 39:1-38, 1977.
6. Alain Denise, Mireille Rgnier, and Mathias Vandenbogaert. Assessing the statistical significance of overrepresented oligonucleotides. In Proceedings of WABI, 2001.
7. E. Eskin, U. Keich, M.S. Gelfand, and P.A. Pevzner. Genome wide analysis of bacterial promoter regions. In Proceedings of the 2003 Pacific Symposium on Biocomputing, 2003.
8. E. Eskin and P. A. Pevzner. Finding composite regulatory patterns in dna sequences. In Special Issue Proceedings of the Tenth International Conference on Intelligent Systems for Molecular Biology (ISMB-2002) Bioinformatics., pages 1:3354-63, 2002.
9. D. J. Galas, M. Eggert, and M. S. Waterman. Rigorous pattern-recognition methods for DNA sequences. Journal of Molecular Biology, 186:117-128, 1985.
10. G. Hertz and G. Stormo. Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. Bioinformatics, 15:563-577, 1999.
11. JD Hughes, PW Estep, S Tavazoie, and GM Church. Computational identification of cis-regulatory elements associated with groups of functionally related genes in saccharomyces cerevisiae. Journal of Molecular Biology, 296(5):1205-14, 2000.
12. U. Keich and P. A. Pevzner. Finding motifs in the twilight zone. In Proceedings of the 6th International Conference on Computational Molecular Biology (RECOMB 2002), 2002.
13. 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, 1993.
14. A. Neuwald, J. Liu, and C. Lawrence. Gibbs motif sampling: Detection of bacterial outer membrane repeats. Protein Science, 4:1618-1632, 1995.
15. P. A. Pevzner and S. Sze. Combinatorial approaches to finding subtle signals in DNA sequences. In Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology, pages 269-278, 2000.
16. M. Sagot. Spelling approximate or repeated motifs using a suffix tree. Lecture Notes in Computer Science, 1380:111-127, 1998.
17. E. Segal, Y. Barash, I. Simon, N. Friedman, and D. Koller. From promoter sequence to expression: A probabilistic framework. In Proceedings of the 6th International Conference on Research in Computational Molecular Biology (RECOMB), 2002.
18. S. Sinha and M. Tompa. Discovery of novel transcription factor binding sites by statistical overrepresentation. Nucleic Acids Research, 30:5549-5560, 2002.
19. S. Sze, M. S. Gelfand, and P. A. Pevzner. Finding subtle motifs in DNA sequences. In Proceedings of Pacific Symposium on Biocomputing, pages 235-246, 2002.
20. M.S. Waterman, R. Arratia, and D.J. Galas. Pattern recognition in several sequences: consensus and alignm ent. Bulletin of Mathematical Biology, 46:515-527, 1984.