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Bayesian Unsupervised Learning of DNA Regulatory Binding Regions英文文献资料.doc

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Bayesian Unsupervised Learning of DNA Regulatory Binding Regions英文文献资料

HindawiPublishingCorporation AdvancesinArti?cialIntelligence Volume2009,ArticleID219743,11pages doi:10.1155/2009/219743 ResearchArticle BayesianUnsupervisedLearningofDNARegulatory BindingRegions JukkaCorander, MagnusEkdahl, andTimoKoski 1 2 3 1 2 3 DepartmentofMathematics,A?boAkademiUniversity,20500Turku,Finland DepartmentofMathematics,UniversityofLink¨oping,58183Link¨oping,Sweden DepartmentofMathematics,TheRoyalInstituteofTechnology,10044Stockholm,Sweden CorrespondenceshouldbeaddressedtoJukkaCorander,jukka.corander@abo.? Received13February2009;Revised6June2009;Accepted2July2009 RecommendedbyDjamelBoucha?ra Identi?cationofregulatorybindingmotifs,thatis,shortspeci?cwords,withinDNAsequencesisacommonlyoccurringproblem incomputationalbioinformatics.Awidevarietyofprobabilisticapproacheshavebeenproposedintheliteraturetoeitherscan forpreviouslyknownmotiftypesortoattemptdenovoidenti?cationofa?xednumber(typicallyone)ofputativemotifs.Most approachesassumetheexistenceofreliablebiodatabaseinformationtobuildprobabilisticaprioridescriptionofthemotifclasses. Examplesofattemptstodoprobabilisticunsupervised learning aboutthenumberofputativedenovomotiftypes andtheir positions within a set of DNA sequences are very rare in the literature. Here we show how such a learning problem can be formulatedusingaBayesianmodelthattargetstosimultaneouslymaximizethemarginallikelihoodofsequencedataarisingunder multiplemotiftypesaswellasunderthebackgroundDNAmodel,whichequalsavariablelengthMarkovchain.Itisdemonstrated howtheadoptedBayesianmodellingstrategycombinedwithrecentlyintroducednonstandardstochasticcomputationtoolsyields amoretractablelearningprocedurethanispossiblewiththestandardMonteCarloapproaches.Improvementsandextensionsof theproposedapproacharealsodiscussed. Copyright?2009JukkaCoranderetal. This is an open access article distributed under the Creative Commons Attribution License,whichpermitsunrestricteduse,distribution,andreproductioninanymedium