PubMed

EXMOTIF: efficient structured motif extraction.

Zhang Y, Zaki MJ.

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

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

Localized Motif Discovery in Gene Regulatory Sequences.

Narang V, Mittal A, Sung WK.

Bioinformatics. 2010 Mar 11. [Epub ahead of print]PMID: 20223835 [PubMed - as supplied by publisher]Related articles

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

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

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

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

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

NestedMICA as an ab initio protein motif discovery tool.

Doğruel M, Down TA, Hubbard TJ.

BMC Bioinformatics. 2008 Jan 14;9:19.PMID: 18194537 [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

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

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

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

W-AlignACE: an improved Gibbs sampling algorithm based on more accurate position weight matrices learned from sequence and gene expression/ChIP-chip data.

Chen X, Guo L, Fan Z, Jiang T.

Bioinformatics. 2008 May 1;24(9):1121-8. Epub 2008 Mar 5.PMID: 18325926 [PubMed - indexed for MEDLINE]Related articlesFree article

PhyME: a software tool for finding motifs in sets of orthologous sequences.

Sinha S.

Methods Mol Biol. 2007;395:309-18.PMID: 17993682 [PubMed - indexed for MEDLINE]Related articles

A specialized learner for inferring structured cis-regulatory modules.

Noto K, Craven M.

BMC Bioinformatics. 2006 Dec 5;7:528.PMID: 17147812 [PubMed - indexed for MEDLINE]Related articlesFree article

HeliCis: a DNA motif discovery tool for colocalized motif pairs with periodic spacing.

Larsson E, Lindahl P, Mostad P.

BMC Bioinformatics. 2007 Oct 28;8:418.PMID: 17963524 [PubMed - indexed for MEDLINE]Related articlesFree article

Extracting transcription factor binding sites from unaligned gene sequences with statistical models.

Lu CC, Yuan WH, Chen TM.

BMC Bioinformatics. 2008 Dec 12;9 Suppl 12:S7.PMID: 19091030 [PubMed - indexed for MEDLINE]Related articlesFree article

CoMoDis: composite motif discovery in mammalian genomes.

Donaldson IJ, Göttgens B.

Nucleic Acids Res. 2007;35(1):e1. Epub 2006 Nov 27.PMID: 17130158 [PubMed - indexed for MEDLINE]Related articlesFree article

Discovering sequence motifs with arbitrary insertions and deletions.

Frith MC, Saunders NF, Kobe B, Bailey TL.

PLoS Comput Biol. 2008 May 9;4(4):e1000071.PMID: 18437229 [PubMed - indexed for MEDLINE]Related articlesFree article