SPA A Probabilistic Algorithm for Spliced Alignment 英文参考文献.docVIP

SPA:AProbabilisticAlgorithmforSpliced Alignment Erik van Nimwegen1,2*,Nicodeme Paul1,2,Robert Sheridan3¤,Mihaela Zavolan1,2 1 Biozentrum, University of Basel, Basel, Switzerland, 2 Swiss Institute of Bioinformatics, Switzerland, 3 The Rockefeller University, New York, New York, United States ofAmerica Recentlarge-scalecDNAsequencingeffortsshowthatelaboratepatternsofsplicevariationareresponsibleformuch oftheproteomediversityinhighereukaryotes.Toobtainanaccurateaccountoftherepertoireofsplicevariants,and togaininsightintothemechanismsofalternativesplicing,itisessentialthatcDNAsareveryaccuratelymappedto theirrespectivegenomes.CurrentlyavailablealgorithmsforcDNA-to-genomealignmentdonotreachthenecessary level of accuracy because they use ad hoc scoring models that cannot correctly trade off the likelihoods of various sequencing errors against the probabilities of different gene structures. Here we develop a Bayesian probabilistic approachtocDNA-to-genomealignment.Genestructuresareassignedpriorprobabilitiesbasedonthelengthsoftheir intronsandexons,andbasedonthesequencesattheirspliceboundaries.Alikelihoodmodelforsequencingerrors takesintoaccounttheratesatwhichmisincorporation,aswellasinsertionsanddeletionsofdifferentlengths,occurs duringsequencing.Theparametersofboththepriorandlikelihoodmodelcanbeautomaticallyestimatedfromaset of cDNAs, thus enabling our method to adapt itself to different organisms and experimental procedures. We implementedourmethodinafastcDNA-to-genomealignmentprogram,SPA,andappliedittotheFANTOM3dataset ofover100,000full-lengthmousecDNAsandadatasetofover20,000full-lengthhumancDNAs.Comparisonwiththe results of four other mapping programs shows that SPA produces alignments of significantly higher quality. In particular,thequalityoftheSPAalignmentsnearspliceboundariesandSPA’smappingofthe59and39endsofthe cDNAs are highly improved, allowing for more accurate identification of transcript starts and ends, and accurate identification of subtle splice variation