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Mining, compressing and classifying with extensible motifs.

Apostolico A, Comin M, Parida L.

Algorithms Mol Biol. 2006 Mar 23;1(1):4.PMID: 16722593 [PubMed]Related articlesFree article

Conservative extraction of over-represented extensible motifs.

Apostolico A, Comin M, Parida L.

Bioinformatics. 2005 Jun;21 Suppl 1:i9-18.PMID: 15961503 [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

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

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

Bases of motifs for generating repeated patterns with wild cards.

Pisanti N, Crochemore M, Grossi R, Sagot MF.

IEEE/ACM Trans Comput Biol Bioinform. 2005 Jan-Mar;2(1):40-50.PMID: 17044163 [PubMed - indexed for MEDLINE]Related articles

Fast model-based protein homology detection without alignment.

Hochreiter S, Heusel M, Obermayer K.

Bioinformatics. 2007 Jul 15;23(14):1728-36. Epub 2007 May 8.PMID: 17488755 [PubMed - indexed for MEDLINE]Related articlesFree article

A combinatorial optimization approach for diverse motif finding applications.

Zaslavsky E, Singh M.

Algorithms Mol Biol. 2006 Aug 17;1:13.PMID: 16916460 [PubMed]Related articlesFree article

Discovering structural motifs using a structural alphabet: application to magnesium-binding sites.

Dudev M, Lim C.

BMC Bioinformatics. 2007 Mar 28;8:106.PMID: 17389049 [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

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

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

Discovering sequence motifs.

Bailey TL.

Methods Mol Biol. 2008;452:231-51. Review.PMID: 18566768 [PubMed - indexed for MEDLINE]Related articles

A novel Bayesian DNA motif comparison method for clustering and retrieval.

Habib N, Kaplan T, Margalit H, Friedman N.

PLoS Comput Biol. 2008 Feb 29;4(2):e1000010.PMID: 18463706 [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

Discovering sequence motifs.

Bailey TL.

Methods Mol Biol. 2007;395:271-92. Review.PMID: 17993680 [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

Bioinformatic characterizations and prediction of K+ and Na+ ion channels effector toxins.

Soli R, Kaabi B, Barhoumi M, El-Ayeb M, Srairi-Abid N.

BMC Pharmacol. 2009 Mar 10;9:4.PMID: 19284552 [PubMed - indexed for MEDLINE]Related articlesFree article

Computational annotation of UTR cis-regulatory modules through Frequent Pattern Mining.

Turi A, Loglisci C, Salvemini E, Grillo G, Malerba D, D'Elia D.

BMC Bioinformatics. 2009 Jun 16;10 Suppl 6:S25.PMID: 19534751 [PubMed - indexed for MEDLINE]Related articlesFree article

Motif discovery in tissue-specific regulatory sequences using directed information.

Rao A, Hero Iii AO, States DJ, Engel JD.

EURASIP J Bioinform Syst Biol. 2007:13853.PMID: 18340376 [PubMed - in process]Related articlesFree article