PMS: A panoptic motif search tool

PLoS ONE

Volumn 8, Issue 12, 2013, Pages

  Dinh, Hieu ^a   Rajasekaran, Sanguthevar ^a  

^a UNIVERSITY OF CONNECTICUT   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; COMPUTER MODEL; DNA SEQUENCE; INFORMATION PROCESSING; INFORMATION SERVICE; PROTEIN MOTIF; WEB BROWSER;

ALGORITHMS; AMINO ACID MOTIFS; DNA; DNA-BINDING PROTEINS; MOLECULAR SEQUENCE DATA; NUCLEOTIDE MOTIFS; SEARCH ENGINE; SOFTWARE;

EID: 84891857502     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0080660     Document Type: Article

References (15)

1. Jonassen I, Collins J, Higgins D (1995) Finding exible patterns in unaligned protein sequences. Protein Science 4: 1587-1595.
2. Bailey TL, Boden M, Buske FA, Frith M, vGrant CE, et al. (2009) MEME SUITE: tools for motif discovery and searching. Nucleic Acids Research 37: W202-W208.
3. Neduva V, Russell R (2006) DILIMOT: discovery of linear motifs in proteins. Nucleic Acids Re- search 34: W350-W355.
4. Davey NE, Shields DC, Edwards RJ (2006) SLiMDisc: short, linear motif discovery, correcting for common evolutionary descent. Nucleic Acids Research 34: 3546-3554.
5. Edwards RJ, Davey NE, Shields DC (2007) SLiMFinder: A probabilistic method for identifying over-represented, convergently evolved, short linear motifs in proteins. PLoS ONE 2: e967.
6. Lieber DS, Elemento O, Tavazoie S (2010) Large-scale discovery and characterization of protein regulatory motifs in eukaryotes. PLoS ONE 5: e14444.
7. Sharma D, Rajasekaran S, Dinh H (2011) An experimental comparison of PMSPrune and other algorithms for motif search. CoRR abs/1108.5217.
8. Rajasekaran S (2009) Computational techniques for motif search. Frontiers in Bioscience 14: 5052-5065.
9. Pisanti N, Carvalho AM, Marsan L, Sagot MF (2006) RISOTTO: Fast extraction of motifs with mismatches. Proceedings of the 7th Latin American Theoretical Informatics Symposium: 757-768.
10. Dinh H, Rajasekaran S, Davila J (2012) qPMS7: A fast Algorithm for finding (l; d)-motifs in DNA and protein sequences. PLoS ONE, 7(7): e41425.
11. Dinh H, Rajasekaran S, Kundeti V (2011) PMS5: an efficient exact algorithm for the (l; d)-motif finding problem. BMC Bioinformatics 12(410).
12. Davila J, Balla S, Rajasekaran S (2007) Fast and practical algorithms for planted (l; d) motif search. IEEE/ACM Transactions on Computational Biology and Bioinformatics: 544-552.
13. Rajasekaran S, Balla S, Huang CH (2005) Exact algorithms for planted motif challenge problems. Journal of Computational Biology 12(8): 1117-1128.
14. Tompa M, Li N, Bailey TL, Church GM, Moor BD, et al. (2005) Assessing computational tools for the discovery of transcription factor binding sites. Nature Biotechnology 23(1): 137-144.
15. Eskin E, Pevzner P (2002) Finding composite regulatory patterns in DNA sequences. Bioinformatics S1: 354-363.