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Analysis of computational approaches for motif discovery.

Li N, Tompa M.

Algorithms Mol Biol. 2006 May 19;1:8.PMID: 16722558 [PubMed]Related articlesFree article

Improved benchmarks for computational motif discovery.

Sandve GK, Abul O, Walseng V, Drabløs F.

BMC Bioinformatics. 2007 Jun 8;8:193.PMID: 17559676 [PubMed - indexed for MEDLINE]Related articlesFree article

Comparative analysis of regulatory motif discovery tools for transcription factor binding sites.

Wei W, Yu XD.

Genomics Proteomics Bioinformatics. 2007 May;5(2):131-42.PMID: 17893078 [PubMed - indexed for MEDLINE]Related articles

Assessment of composite motif discovery methods.

Klepper K, Sandve GK, Abul O, Johansen J, Drablos F.

BMC Bioinformatics. 2008 Feb 26;9:123.PMID: 18302777 [PubMed - indexed for MEDLINE]Related articlesFree article

Identification of degenerate motifs using position restricted selection and hybrid ranking combination.

Peng CH, Hsu JT, Chung YS, Lin YJ, Chow WY, Hsu DF, Tang CY.

Nucleic Acids Res. 2006;34(22):6379-91. Epub 2006 Nov 27.PMID: 17130169 [PubMed - indexed for MEDLINE]Related articlesFree article

Fast motif recognition via application of statistical thresholds.

Boucher C, King J.

BMC Bioinformatics. 2010 Jan 18;11 Suppl 1:S11.PMID: 20122182 [PubMed - in process]Related articlesFree article

New scoring schema for finding motifs in DNA Sequences.

Zare-Mirakabad F, Ahrabian H, Sadeghi M, Nowzari-Dalini A, Goliaei B.

BMC Bioinformatics. 2009 Mar 20;10:93.PMID: 19302709 [PubMed - indexed for MEDLINE]Related articlesFree article

MTAP: the motif tool assessment platform.

Quest D, Dempsey K, Shafiullah M, Bastola D, Ali H.

BMC Bioinformatics. 2008 Aug 12;9 Suppl 9:S6.PMID: 18793470 [PubMed - indexed for MEDLINE]Related articlesFree article

MEME SUITE: tools for motif discovery and searching.

Bailey TL, Boden M, Buske FA, Frith M, Grant CE, Clementi L, Ren J, Li WW, Noble WS.

Nucleic Acids Res. 2009 Jul 1;37(Web Server issue):W202-8. Epub 2009 May 20.PMID: 19458158 [PubMed - indexed for MEDLINE]Related articlesFree article

A hybrid model for robust detection of transcription factor binding sites.

Gunewardena S, Zhang Z.

Bioinformatics. 2008 Feb 15;24(4):484-91. Epub 2008 Jan 9.PMID: 18184687 [PubMed - indexed for MEDLINE]Related articlesFree article

Seeder: discriminative seeding DNA motif discovery.

Fauteux F, Blanchette M, Strömvik MV.

Bioinformatics. 2008 Oct 15;24(20):2303-7. Epub 2008 Aug 21.PMID: 18718942 [PubMed - indexed for MEDLINE]Related articlesFree article

Eukaryotic transcription factor binding sites--modeling and integrative search methods.

Hannenhalli S.

Bioinformatics. 2008 Jun 1;24(11):1325-31. Epub 2008 Apr 21. Review.PMID: 18426806 [PubMed - indexed for MEDLINE]Related articlesFree article

A survey of DNA motif finding algorithms.

Das MK, Dai HK.

BMC Bioinformatics. 2007 Nov 1;8 Suppl 7:S21. Review.PMID: 18047721 [PubMed - indexed for MEDLINE]Related articlesFree article

Discovering motifs in ranked lists of DNA sequences.

Eden E, Lipson D, Yogev S, Yakhini Z.

PLoS Comput Biol. 2007 Mar 23;3(3):e39.PMID: 17381235 [PubMed - indexed for MEDLINE]Related articlesFree article

Using DNA duplex stability information for transcription factor binding site discovery.

Gordân R, Hartemink AJ.

Pac Symp Biocomput. 2008:453-64.PMID: 18229707 [PubMed - indexed for MEDLINE]Related articlesFree article

OHMM: a Hidden Markov Model accurately predicting the occupancy of a transcription factor with a self-overlapping binding motif.

Drawid A, Gupta N, Nagaraj VH, Gélinas C, Sengupta AM.

BMC Bioinformatics. 2009 Jul 7;10:208.PMID: 19583839 [PubMed - indexed for MEDLINE]Related articlesFree article

FISim: a new similarity measure between transcription factor binding sites based on the fuzzy integral.

Garcia F, Lopez FJ, Cano C, Blanco A.

BMC Bioinformatics. 2009 Jul 20;10:224.PMID: 19615102 [PubMed - indexed for MEDLINE]Related articlesFree article

Transcription factor and microRNA motif discovery: the Amadeus platform and a compendium of metazoan target sets.

Linhart C, Halperin Y, Shamir R.

Genome Res. 2008 Jul;18(7):1180-9. Epub 2008 Apr 14.PMID: 18411406 [PubMed - indexed for MEDLINE]Related articlesFree article

Bioinformatic identification of novel putative photoreceptor specific cis-elements.

Danko CG, McIlvain VA, Qin M, Knox BE, Pertsov AM.

BMC Bioinformatics. 2007 Oct 22;8:407.PMID: 17953763 [PubMed - indexed for MEDLINE]Related articlesFree article

Detection of generic spaced motifs using submotif pattern mining.

Wijaya E, Rajaraman K, Yiu SM, Sung WK.

Bioinformatics. 2007 Jun 15;23(12):1476-85. Epub 2007 May 5.PMID: 17483509 [PubMed - indexed for MEDLINE]Related articlesFree article