MatureBayes A Probabilistic Algorithm for Identifying the Mature miRNA within Novel Precursors 英文参考文献.docVIP

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MatureBayes A Probabilistic Algorithm for Identifying the Mature miRNA within Novel Precursors 英文参考文献.doc

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MatureBayes A Probabilistic Algorithm for Identifying the Mature miRNA within Novel Precursors 英文参考文献

MatureBayes: AProbabilisticAlgorithmforIdentifying theMaturemiRNAwithinNovelPrecursors KaterinaGkirtzou1,2,IoannisTsamardinos1,2,PanagiotisTsakalides1,2,PanayiotaPoirazi3* 1ComputerScienceDepartment,UniversityofCrete,Heraklion,Greece,2InstituteofComputerScience(ICS),FoundationforResearchandTechnology-Hellas(FORTH), Heraklion,Greece,3InstituteofMolecularBiologyandBiotechnology(IMBB),FoundationforResearchandTechnology-Hellas(FORTH),Heraklion,Greece Abstract Background: MicroRNAs (miRNAs) are small, single stranded RNAs with a key role in post-transcriptional regulation of thousandsofgenesacrossnumerousspecies.Whileseveralcomputationalmethodsarecurrentlyavailableforidentifying miRNAgenes,accuratepredictionofthematuremiRNAremainsachallenge.Existingapproachesfallshortinpredictingthe locationofmaturemiRNAsbutalsoinfindingthefunctionalstrand(s)ofmiRNAprecursors. Methodology/Principal Findings: Here, we present a computational tool that incorporates a Naive Bayes classifier to identifymaturemiRNAcandidatesbasedonsequenceandsecondarystructureinformationoftheirmiRNAprecursors.We takeintoaccountbothpositive(truematuremiRNAs)andnegative(same-sizenon-maturemiRNAsequences)examplesto optimizesensitivity aswell asspecificity. Ourmethodcanaccurately predictthestart positionof experimentally verified maturemiRNAsforbothhumanandmouse,achievingasignificantlylarger(oftendouble)performanceaccuracycompared withtwoexistingmethods.Moreover,themethodexhibitsaveryhighgeneralizationperformanceonmiRNAsfromtwo otherorganisms.Moreimportantly,ourmethodprovidesdirectevidenceaboutthefeaturesofmiRNAprecursorswhich maydeterminethelocationofthematuremiRNA.Wefindthatthetripletofpositions7,8and9fromthematuremiRNA end towards the closest hairpin have the largest discriminatory power, are relatively conserved in terms of sequence composition(mostlycontainaUracil)andarelocatedwithinorinverycloseproximitytothehairpinloop,suggestingthe existenceofapossiblerecognitionsiteforDicerandassociatedproteins. Con