qPMS7: A fast algorithm for finding (ℓ, d)-motifs in DNA and protein sequences

PLoS ONE

Volumn 7, Issue 7, 2012, Pages

  Dinh, Hieu ^a   Rajasekaran, Sanguthevar ^a   Davila, Jaime ^b  

^a University of Connecticut   (United States)

^b MAYO CLINIC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; COMPUTER PROGRAM; DATA ANALYSIS; DNA SEQUENCE; INTERMETHOD COMPARISON; INTERNET; MOLECULAR MODEL; ONLINE SYSTEM; PROBLEM SOLVING; PROTEIN MOTIF; QUORUM PLANTED MOTIF SEARCH ALGORITHM; SEQUENCE ANALYSIS;

ALGORITHMS; AMINO ACID MOTIFS; ANIMALS; HUMANS; INTERNET; SEQUENCE ANALYSIS, DNA; SEQUENCE ANALYSIS, PROTEIN; SOFTWARE;

EID: 84864189089     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0041425     Document Type: Article

References (28)

1. Laurent D, Philipp B, (1997) Searching for regulatory elements in human noncoding sequences. Current Opinion in Structural Biology 7: 399-406.
2. Rajasekaran S, (2009) Computational techniques for motif search. Frontiers in Bioscience 14: 5052-5065.
3. Bandyopadhyay S, Sahni S, Rajasekaran S, (2012) Pms6: A faster algorithm for motif discovery. In: Proceedings of the second IEEE International Conference on Computational Advances in Bio and Medical Sciences (ICCABS 2012): 1-6.
4. Dinh H, Rajasekaran S, Kundeti V, (2011) Pms5: an efficient exact algorithm for the (l; d)-motiffinding problem. BMC Bioinformatics 12.
5. Davila J, Balla S, Rajasekaran S, (2007) Pampa: An improved branch and bound algorithm for planted (l, d) motif search. Technical report.
6. Davila J, Balla S, Rajasekaran S, (2007) Fast and practical algorithms for planted (l; d) motif search. In: IEEE/ACM Transactions on Computational Biology and Bioinformatics. pp. pp 544-552.
7. Rajasekaran S, Balla S, Huang CH, (2005) Exact algorithms for planted motif challenge problems. Journal of Computational Biology 12: 1117-1128.
8. Chin F, Leung H, (2005) Algorithms for discovering long motifs. In: Proceedings of the Third Asia-Pacific Bioinformatics Conference (APBC2005), Singapore. pp. pp 261-271.
9. Pisanti N, Carvalho A, Marsan L, Sagot MF, (2006) Risotto: Fast extraction of motifs with mismatches. In: Proceedings of the 7th Latin American Theoretical Informatics Symposium. pp. pp 757-768.
10. Blanchette M, Schwikowski B, Tompa M, (2000) An exact algorithm to identify motifs in or-thologous sequences from multiple species. In: Proceedings of Eighth International Conference on Intelligent Systems for Molecular Biology. pp. pp 37-45.
11. Brazma A, Jonassen I, Vilo J, Ukkonen E, (1998) Predicting gene regulatory elements in silico on a genomic scale. Genome Research 15: 1202-1215.
12. Eskin E, Pevzner P, (2002) Finding composite regulatory patterns in dna sequences. Bioinformatics S1: 354-363.
13. Galas DJ, Eggert M, Waterman MS, (1985) Rigorous pattern-recognition methods for dna sequences: Analysis of promoter sequences from escherichia coli. Journal of Molecular Biology 186: 117-128.
14. Sinha S, Tompa M, (2000) A statistical method for finding transcription factor binding sites. In: Proceedings of Eighth International Conference on Intelligent Systems for Molecular Biology. pp. pp 344-354.
15. Staden R, (1989) Methods for discovering novel motifs in nucleic acid sequences. Computer Applications in the Biosciences 5: 293-298.
16. Tompa M, (1999) An exact method for finding short motifs in sequences, with application to the ribosome binding site problem. In: Proc. Seventh International Conference on Intelligent Systems for Molecular Biology. pp. pp 262-271.
17. Helden J, André B, Collado-Vides J, (1998) Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies. Journal of Molecular Biology 281: 827-842.
18. Bailey T, Elkan C, (1994) Fitting a mixture model by expectation maximization to discover motifs in biopolymers. In: Proceedings of Second International Conference on Intelligent Systems for Molecular Biology. pp. pp 28-36.
19. Buhler J, Tompa M, (2001) Finding motifs using random projections. In: Proceedings of Fifth Annual International Conference on Computational Molecular Biology (RECOMB). pp. pp 69-76.
20. Lawrence CE, Altschul SF, Boguski MS, Liu JS, Neuwald AF, et al. (1993) Detecting subtle sequence signals: a gibbs sampling strategy for multiple alignment. Science 262: 208-214.
21. Pevzner P, Sze SH, (2000) Combinatorial approaches to finding subtle signals in dna sequences. In: Proceedings of Eighth International Conference on Intelligent Systems for Molecular Biology. pp. pp 269-278.
22. Rocke E, Tompa M, (1998) An algorithm for finding novel gapped motifs in dna sequences. In: Proceedings of Second International Conference on Computational Molecular Biology (RECOMB). pp. pp 228-233.
23. Keich U, Pevzner P, (2002) Finding motifs in the twilight zone. Bioinformatics 18: 1374-1381.
24. Price A, Ramabhadran S, Pevzner PA, (2003) Finding subtle motifs by branching from sample strings. Bioinformatics 1: 1-7.
25. Hertz G, Stormo G, (1999) Identifying dna and protein patterns with statistically significant alignments of multiple sequences. Bioinformatics 15: 563-577.
26. Kuksa P, Pavlovic V, (2010) Efficient motif finding algorithms for large-alphabet inputs. BMC Bioinformatics 11.
27. Blanchette M, (2001) Algorithms for phylogenetic footprinting. In: Proceedings of Fifth International Conference Computational Biology (RECOMB 2001): 49-58.
28. Tompa M, Li N, Bailey T, Church G, Moor BD, et al. (2005) Assessing computational tools for the discovery of transcription factor binding sites. Nature Biotechnology 23: 137-144.