PMS5: An efficient exact algorithm for the (ℓ, d)-motif finding problem

BMC Bioinformatics

Volumn 12, Issue , 2011, Pages

  Dinh, Hieu ^a   Rajasekaran, Sanguthevar ^a   Kundeti, Vamsi K ^a  

^a UNIVERSITY OF CONNECTICUT   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL SEQUENCES; EFFICIENT EXACT ALGORITHMS; EXACT ALGORITHMS; EXPONENTIAL TIME; FAST ALGORITHMS; REGULATORY ELEMENTS; TRANSCRIPTION FACTOR BINDING SITES; WORST CASE SCENARIO;

APPROXIMATION ALGORITHMS;

DNA; DNA BINDING PROTEIN;

ALGORITHM; ARTICLE; BIOLOGY; CHEMISTRY; HUMAN; METABOLISM; PROTEIN BINDING; REGULATORY SEQUENCE;

ALGORITHMS; COMPUTATIONAL BIOLOGY; DNA; DNA-BINDING PROTEINS; HUMANS; PROTEIN BINDING; REGULATORY ELEMENTS, TRANSCRIPTIONAL;

EID: 80054807741     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-12-410     Document Type: Article

References (25)

1. Rajasekaran S. Computational techniques for motif search. Frontiers in Bioscience 2009, 14:5052-5065. 10.2741/3586, 19482604.
2. Bailey T, Elkan C. Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proceedings of Second International Conference on Intelligent Systems for Molecular Biology 1994, 28-36.
3. Buhler J, Tompa M. Finding motifs using random projections. Proceedings of Fifth Annual International Conference on Computational Molecular Biology (RECOMB) 2001,
4. Lawrence CE, Altschul SF, Boguski MS, Liu JS, Neuwald AF, Wootton JC. Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment. Science 1993, 262:208-214. 10.1126/science.8211139, 8211139.
5. Pevzner P, Sze SH. Combinatorial approaches to finding subtle signals in DNA sequences. Proceedings of Eighth International Conference on Intelligent Systems for Molecular Biology 2000, 269-278.
6. Rocke E, Tompa M. An algorithm for finding novel gapped motifs in DNA sequences. Proceedings of Second International Conference on Computational Molecular Biology (RECOMB) 1998, 228-233.
7. Keich U, Pevzner P. Finding motifs in the twilight zone. Bioinformatics 2002, 18:1374-1381. 10.1093/bioinformatics/18.10.1374, 12376382.
8. Price A, Ramabhadran S, Pevzner PA. Finding subtle motifs by branching from sample strings. Bioinformatics 2003, 1:1-7.
9. Hertz G, Stormo G. Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. Bioinformatics 1999, 15:563-577. 10.1093/bioinformatics/15.7.563, 10487864.
10. Davila J, Balla S, Rajasekaran S. Pampa: An Improved Branch and Bound Algorithm for Planted (l, d) Motif Search. Tech. rep 2007,
11. Rajasekaran S, Balla S, Huang CH. Exact algorithms for planted motif challenge problems. Journal of Computational Biology 2005, 12(8):1117-1128. 10.1089/cmb.2005.12.1117, 16241901.
12. Blanchette M, Schwikowski B, Tompa M. An exact algorithm to identify motifs in orthologous sequences from multiple species. Proceedings of Eighth International Conference on Intelligent Systems for Molecular Biology 2000, 37-45.
13. Eskin E, Pevzner P. Finding composite regulatory patterns in DNA sequences. Bioinformatics 2002, S1:354-363.
14. Brazma A, Jonassen I, Vilo J, Ukkonen E. Predicting gene regulatory elements in silico on a genomic scale. Genome Research 1998, 15:1202-1215.
15. Galas DJ, Eggert M, Waterman MS. Rigorous pattern-recognition methods for DNA sequences: Analysis of promoter sequences from Escherichia coli. Journal of Molecular Biology 1985, 186:117-128. 10.1016/0022-2836(85)90262-1, 3908689.
16. Sinha S, Tompa M. A statistical method for finding transcription factor binding sites. Proceedings of Eighth International Conference on Intelligent Systems for Molecular Biology 2000, 344-354.
17. Staden R. Methods for discovering novel motifs in nucleic acid sequences. Computer Applications in the Biosciences 1989, 5(4):293-298.
18. Tompa M. An exact method for finding short motifs in sequences, with application to the ribosome binding site problem. Proc. Seventh International Conference on Intelligent Systems for Molecular Biology 1999, 262-271.
19. van Helden J, André B, Collado-Vides J. Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies. Journal of Molecular Biology 1998, 281(5):827-842. 10.1006/jmbi.1998.1947, 9719638.
20. Chin F, Leung H. Algorithms for Discovering Long Motifs. Proceedings of the Third Asia-Pacific Bioinformatics Conference (APBC2005), Singapore 2005, 261-271.
21. Pisanti N, Carvalho A, Marsan L, Sagot MF. RISOTTO: Fast extraction of motifs with mismatches. Proceedings of the 7th Latin American Theoretical Informatics Symposium 2006, 757-768.
22. Davila J, Balla S, Rajasekaran S. Fast and practical algorithms for planted (l,d) motif search. IEEE/ACM Transactions on Computational Biology and Bioinformatics 2007, 544-552.
23. Blanchette M. Algorithms for Phylogenetic Footprinting. Proceedings of Fifth International Conference Computational Biology (RECOMB 2001) 2001,
24. Tompa M, Li N, Bailey T, Church G, Moor BD, Eskin E, Favorov A, Frith M, Fu Y, Kent W, Makeev V, Mironov A, Noble W, Pavesi G, Pesole G, Regnier M, Simonis N, Sinha S, Thijs G, van Helden J, Vandenbogaert M, Weng Z, Workman C, Ye C, Zhu Z. Assessing Computational Tools for the Discovery of Transcription Factor Binding Sites. Nature Biotechnology 2005, 23:137-144. 10.1038/nbt1053, 15637633.
25. Sharma D, Rajasekaran S, Dinh H. An Experimental Comparison of PMSPrune and Other Algorithms for Motif Search. CoRR abs/1108.5217 2011,