Discovering cis-Regulatory RNAs in Shewanella Genomes by Support Vector Machines 英文参考文献.docVIP

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Discovering cis-Regulatory RNAs in Shewanella Genomes by Support Vector Machines 英文参考文献.doc

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Discovering cis-Regulatory RNAs in Shewanella Genomes by Support Vector Machines 英文参考文献

Discoveringcis-RegulatoryRNAsinShewanella Genomes bySupportVectorMachines XingXu,YongmeiJi¤,GaryD.Stormo* DepartmentofGenetics,WashingtonUniversitySchoolofMedicine,St.Louis,Missouri,UnitedStatesofAmerica Abstract Anincreasingnumberofcis-regulatoryRNAelementshavebeenfoundtoregulategeneexpressionpost-transcriptionallyin various biological processes in bacterial systems. Effective computational tools for large-scale identification of novel regulatoryRNAsarestronglydesiredtofacilitateourexplorationofgeneregulationmechanismsandregulatorynetworks. WepresentanewcomputationalprogramnamedRSSVM(RNASampler+SupportVectorMachine),whichemploysSupport VectorMachines(SVMs)forefficientidentificationoffunctionalRNAmotifsfromrandomRNAsecondarystructures.RSSVM usesasetofdistinctivefeaturestorepresentthecommonRNAsecondarystructureandstructuralalignmentpredictedby RNASampler,atoolforaccuratecommonRNAsecondarystructureprediction,andistrainedwithfunctionalRNAsfroma varietyofbacterialRNAmotif/genefamiliescoveringawiderangeofsequenceidentities.Whentestedonalargenumberof known and random RNA motifs, RSSVM shows a significantly higher sensitivity than other leading RNA identification programs while maintaining the same false positive rate. RSSVM performs particularly well on sets with low sequence identities.ThecombinationofRNASamplerandRSSVMprovidesanew,fast,andefficientpipelineforlarge-scalediscovery ofregulatoryRNAmotifs.WeappliedRSSVMtomultipleShewanellagenomesandidentifiedputativeregulatoryRNAmotifs inthe59untranslatedregions(UTRs)inS.oneidensis,animportantbacterialorganismwithextraordinaryrespiratoryand metalreducing abilities andgreatpotential forbioremediation andalternativeenergy generation.From 1002 setsof 59- UTRsoforthologousoperons,weidentified166putativeregulatoryRNAmotifs,including17ofthe19knownRNAmotifs fromRfam,anadditional21RNAmotifsthataresupportedbyliteratureevidence,72RNAmotifsoverlappingpredicted transcriptionterminatorsorattenuators,andothercandidateregulatoryRNAmo