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Exact distribution of a pattern in a set of random sequences generated by a Markov source: applications to biological data.

Nuel G, Regad L, Martin J, Camproux AC.

Algorithms Mol Biol. 2010 Jan 26;5:15.PMID: 20205909 [PubMed]Free PMC ArticleFree textRelated citations

Faster exact Markovian probability functions for motif occurrences: a DFA-only approach.

Ribeca P, Raineri E.

Bioinformatics. 2008 Dec 15;24(24):2839-48. Epub 2008 Oct 9.PMID: 18845582 [PubMed - indexed for MEDLINE]Free ArticleRelated citations

Deriving non-homogeneous DNA Markov chain models by cluster analysis algorithm minimizing multiple alignment entropy.

Borodovsky M, Peresetsky A.

Comput Chem. 1994 Sep;18(3):259-67.PMID: 7952897 [PubMed - indexed for MEDLINE]Related citations

Calculating the exact probability of language-like patterns in biomolecular sequences.

Atteson K.

Proc Int Conf Intell Syst Mol Biol. 1998;6:17-24.PMID: 9783205 [PubMed - indexed for MEDLINE]Related citations

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]Free ArticleRelated citations

Exact computation of pattern probabilities in random sequences generated by Markov chains.

Kleffe J, Langbecker U.

Comput Appl Biosci. 1990 Oct;6(4):347-53.PMID: 2257495 [PubMed - indexed for MEDLINE]Related citations

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]Free PMC ArticleFree textRelated citations

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]Free PMC ArticleFree textRelated citations

Bayesian coestimation of phylogeny and sequence alignment.

Lunter G, Miklós I, Drummond A, Jensen JL, Hein J.

BMC Bioinformatics. 2005 Apr 1;6:83.PMID: 15804354 [PubMed - indexed for MEDLINE]Free PMC ArticleFree textRelated citations

Towards a better solution to the shortest common supersequence problem: the deposition and reduction algorithm.

Ning K, Leong HW.

BMC Bioinformatics. 2006 Dec 12;7 Suppl 4:S12.PMID: 17217504 [PubMed - indexed for MEDLINE]Free PMC ArticleFree textRelated citations

An algebraic geometry approach to protein structure determination from NMR data.

Wang L, Mettu RR, Donald BR.

Proc IEEE Comput Syst Bioinform Conf. 2005:235-46.PMID: 16447981 [PubMed - indexed for MEDLINE]Related citations

Multiple pattern matching: a Markov chain approach.

Lladser ME, Betterton MD, Knight R.

J Math Biol. 2008 Jan;56(1-2):51-92. Epub 2007 Aug 1.PMID: 17668213 [PubMed - indexed for MEDLINE]Related citations

Conditional rate derivation in the presence of intervening variables using a Markov chain.

Shachtman RH, Schoenfelder JR, Hogue CJ.

Oper Res. 1982 Nov-Dec;30(6):1070-81.PMID: 10259644 [PubMed - indexed for MEDLINE]Related citations

Protein secondary structure prediction for a single-sequence using hidden semi-Markov models.

Aydin Z, Altunbasak Y, Borodovsky M.

BMC Bioinformatics. 2006 Mar 30;7:178.PMID: 16571137 [PubMed - indexed for MEDLINE]Free PMC ArticleFree textRelated citations

Kernel-imbedded Gaussian processes for disease classification using microarray gene expression data.

Zhao X, Cheung LW.

BMC Bioinformatics. 2007 Feb 28;8:67.PMID: 17328811 [PubMed - indexed for MEDLINE]Free PMC ArticleFree textRelated citations

A linear memory algorithm for Baum-Welch training.

Miklós I, Meyer IM.

BMC Bioinformatics. 2005 Sep 19;6:231.PMID: 16171529 [PubMed - indexed for MEDLINE]Free PMC ArticleFree textRelated citations

Representative transcript sets for evaluating a translational initiation sites predictor.

Zeng J, Alhajj R, Demetrick DJ.

BMC Bioinformatics. 2009 Jul 2;10:206.PMID: 19573244 [PubMed - indexed for MEDLINE]Free PMC ArticleFree textRelated citations

Background rareness-based iterative multiple sequence alignment algorithm for regulatory element detection.

Narasimhan C, LoCascio P, Uberbacher E.

Bioinformatics. 2003 Oct 12;19(15):1952-63.PMID: 14555629 [PubMed - indexed for MEDLINE]Free ArticleRelated citations

ProClust: improved clustering of protein sequences with an extended graph-based approach.

Pipenbacher P, Schliep A, Schneckener S, Schönhuth A, Schomburg D, Schrader R.

Bioinformatics. 2002;18 Suppl 2:S182-91.PMID: 12386002 [PubMed - indexed for MEDLINE]Free ArticleRelated citations

Finding the biologically optimal alignment of multiple sequences.

Mamitsuka H.

Artif Intell Med. 2005 Sep-Oct;35(1-2):9-18.PMID: 16051477 [PubMed - indexed for MEDLINE]Related citations