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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

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

NestedMICA: sensitive inference of over-represented motifs in nucleic acid sequence.

Down TA, Hubbard TJ.

Nucleic Acids Res. 2005 Mar 10;33(5):1445-53. Print 2005.PMID: 15760844 [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

CompariMotif: quick and easy comparisons of sequence motifs.

Edwards RJ, Davey NE, Shields DC.

Bioinformatics. 2008 May 15;24(10):1307-9. Epub 2008 Mar 28.PMID: 18375965 [PubMed - indexed for MEDLINE]Related articlesFree article

Finding motifs with insufficient number of strong binding sites.

Leung HC, Chin FY, Yiu SM, Rosenfeld R, Tsang WW.

J Comput Biol. 2005 Jul-Aug;12(6):686-701.PMID: 16108711 [PubMed - indexed for MEDLINE]Related articles

Regulatory motif finding by logic regression.

Keles S, van der Laan MJ, Vulpe C.

Bioinformatics. 2004 Nov 1;20(16):2799-811. Epub 2004 May 27.PMID: 15166027 [PubMed - indexed for MEDLINE]Related articlesFree article

FunClust: a web server for the identification of structural motifs in a set of non-homologous protein structures.

Ausiello G, Gherardini PF, Marcatili P, Tramontano A, Via A, Helmer-Citterich M.

BMC Bioinformatics. 2008 Mar 26;9 Suppl 2:S2.PMID: 18387204 [PubMed - indexed for MEDLINE]Related articlesFree article

PhyloGibbs: a Gibbs sampling motif finder that incorporates phylogeny.

Siddharthan R, Siggia ED, van Nimwegen E.

PLoS Comput Biol. 2005 Dec;1(7):e67. Epub 2005 Dec 9.PMID: 16477324 [PubMed - indexed for MEDLINE]Related articlesFree article

MEME: discovering and analyzing DNA and protein sequence motifs.

Bailey TL, Williams N, Misleh C, Li WW.

Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W369-73.PMID: 16845028 [PubMed - indexed for MEDLINE]Related articlesFree article

A correlated motif approach for finding short linear motifs from protein interaction networks.

Tan SH, Hugo W, Sung WK, Ng SK.

BMC Bioinformatics. 2006 Nov 16;7:502.PMID: 17107624 [PubMed - indexed for MEDLINE]Related articlesFree article

ARCS-Motif: discovering correlated motifs from unaligned biological sequences.

Zhang S, Su W, Yang J.

Bioinformatics. 2009 Jan 15;25(2):183-9. Epub 2008 Dec 9.PMID: 19073591 [PubMed - indexed for MEDLINE]Related articles

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

SEAM: a Stochastic EM-type Algorithm for Motif-finding in biopolymer sequences.

Bi C.

J Bioinform Comput Biol. 2007 Feb;5(1):47-77.PMID: 17477491 [PubMed - indexed for MEDLINE]Related articles

Gapped alignment of protein sequence motifs through Monte Carlo optimization of a hidden Markov model.

Neuwald AF, Liu JS.

BMC Bioinformatics. 2004 Oct 25;5:157.PMID: 15504234 [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

An artificial intelligence approach to motif discovery in protein sequences: application to steriod dehydrogenases.

Bailey TL, Baker ME, Elkan CP.

J Steroid Biochem Mol Biol. 1997 May;62(1):29-44.PMID: 9366496 [PubMed - indexed for MEDLINE]Related articles

Motif extraction and protein classification.

Kunik V, Solan Z, Edelman S, Ruppin E, Horn D.

Proc IEEE Comput Syst Bioinform Conf. 2005:80-5.PMID: 16447965 [PubMed - indexed for MEDLINE]Related articles

Compression-based classification of biological sequences and structures via the Universal Similarity Metric: experimental assessment.

Ferragina P, Giancarlo R, Greco V, Manzini G, Valiente G.

BMC Bioinformatics. 2007 Jul 13;8:252.PMID: 17629909 [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