PubMed

SMOTIF: efficient structured pattern and profile motif search.

Zhang Y, Zaki MJ.

Algorithms Mol Biol. 2006 Nov 21;1:22.PMID: 17118189 [PubMed]Related articlesFree article

EXMOTIF: efficient structured motif extraction.

Zhang Y, Zaki MJ.

Algorithms Mol Biol. 2006 Nov 16;1:21.PMID: 17109757 [PubMed]Related articlesFree article

MATLIGN: a motif clustering, comparison and matching tool.

Kankainen M, Löytynoja A.

BMC Bioinformatics. 2007 Jun 8;8:189.PMID: 17559640 [PubMed - indexed for MEDLINE]Related articlesFree article

Randomized algorithms for motif detection.

Wang L, Dong L.

J Bioinform Comput Biol. 2005 Oct;3(5):1039-52.PMID: 16278946 [PubMed - indexed for MEDLINE]Related articles

Discriminative motif discovery in DNA and protein sequences using the DEME algorithm.

Redhead E, Bailey TL.

BMC Bioinformatics. 2007 Oct 15;8:385.PMID: 17937785 [PubMed - indexed for MEDLINE]Related articlesFree article

Efficient exact motif discovery.

Marschall T, Rahmann S.

Bioinformatics. 2009 Jun 15;25(12):i356-64.PMID: 19478010 [PubMed - indexed for MEDLINE]Related articlesFree article

rMotifGen: random motif generator for DNA and protein sequences.

Rouchka EC, Hardin CT.

BMC Bioinformatics. 2007 Aug 7;8:292.PMID: 17683637 [PubMed - indexed for MEDLINE]Related articlesFree article

HIGEDA: a hierarchical gene-set genetics based algorithm for finding subtle motifs in biological sequences.

Le T, Altman T, Gardiner K.

Bioinformatics. 2010 Feb 1;26(3):302-9. Epub 2009 Dec 8.PMID: 19996163 [PubMed - in process]Related articles

High-performance exact algorithms for motif search.

Rajasekaran S, Balla S, Huang CH, Thapar V, Gryk M, Maciejewski M, Schiller M.

J Clin Monit Comput. 2005 Oct;19(4-5):319-28.PMID: 16328946 [PubMed - indexed for MEDLINE]Related articles

Voting algorithms for the motif finding problem.

Liu X, Ma B, Wang L.

Comput Syst Bioinformatics Conf. 2008;7:37-47.PMID: 19642267 [PubMed - indexed for MEDLINE]Related articles

Cis-motifs upstream of the transcription and translation initiation sites are effectively revealed by their positional disequilibrium in eukaryote genomes using frequency distribution curves.

Berendzen KW, Stüber K, Harter K, Wanke D.

BMC Bioinformatics. 2006 Nov 30;7:522.PMID: 17137509 [PubMed - indexed for MEDLINE]Related articlesFree article

Searching RNA motifs and their intermolecular contacts with constraint networks.

Thébault P, de Givry S, Schiex T, Gaspin C.

Bioinformatics. 2006 Sep 1;22(17):2074-80. Epub 2006 Jul 4.PMID: 16820426 [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

Prediction of cis-regulatory elements: from high-information content analysis to motif identification.

Li G, Lu J, Olman V, Xu Y.

J Bioinform Comput Biol. 2007 Aug;5(4):817-38.PMID: 17787058 [PubMed - indexed for MEDLINE]Related articles

BEAM: a beam search algorithm for the identification of cis-regulatory elements in groups of genes.

Carlson JM, Chakravarty A, Gross RH.

J Comput Biol. 2006 Apr;13(3):686-701.PMID: 16706719 [PubMed - indexed for MEDLINE]Related articles

A profile-based deterministic sequential Monte Carlo algorithm for motif discovery.

Liang KC, Wang X, Anastassiou D.

Bioinformatics. 2008 Jan 1;24(1):46-55. Epub 2007 Nov 17.PMID: 18024972 [PubMed - indexed for MEDLINE]Related articlesFree article

Exact p-value calculation for heterotypic clusters of regulatory motifs and its application in computational annotation of cis-regulatory modules.

Boeva V, Clément J, Régnier M, Roytberg MA, Makeev VJ.

Algorithms Mol Biol. 2007 Oct 10;2:13.PMID: 17927813 [PubMed]Related articlesFree article

CompMoby: comparative MobyDick for detection of cis-regulatory motifs.

Chaivorapol C, Melton C, Wei G, Yeh RF, Ramalho-Santos M, Blelloch R, Li H.

BMC Bioinformatics. 2008 Oct 27;9:455.PMID: 18950538 [PubMed - indexed for MEDLINE]Related articlesFree article

Variable structure motifs for transcription factor binding sites.

Reid JE, Evans KJ, Dyer N, Wernisch L, Ott S.

BMC Genomics. 2010 Jan 14;11:30.PMID: 20074339 [PubMed - in process]Related articlesFree article

DISCOVER: a feature-based discriminative method for motif search in complex genomes.

Fu W, Ray P, Xing EP.

Bioinformatics. 2009 Jun 15;25(12):i321-9.PMID: 19478006 [PubMed - indexed for MEDLINE]Related articlesFree article