smyRNA A Novel Ab Initio ncRNA Gene Finder 英文参考文献.docVIP

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smyRNA A Novel Ab Initio ncRNA Gene Finder 英文参考文献.doc

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smyRNA A Novel Ab Initio ncRNA Gene Finder 英文参考文献

smyRNA:ANovelAbInitioncRNAGeneFinder RahelehSalari1.,CagriAksay1.,EmreKarakoc2,PeterJ.Unrau3,ImanHajirasouliha1,S.CenkSahinalp1* 1SchoolofComputingScience,SimonFraserUniversity,Burnaby,BritishColumbia,Canada,2SchoolofComputerScience,UniversityofWaterloo,Waterloo,Ontario, Canada,3DepartmentofMolecularBiologyandBiochemistry,SimonFraserUniversity,Burnaby,BritishColumbia,Canada Abstract Background: Non-coding RNAs (ncRNAs) have important functional roles in the cell: for example, they regulate gene expression by means of establishing stable joint structures with target mRNAs via complementary sequence motifs. SequencemotifsarealsoimportantdeterminantsofthestructureofncRNAs.AlthoughncRNAsareabundant,discovering novelncRNAsongenomesequenceshasproventobeahardtask;inparticularpastattemptsforabinitioncRNAsearch mostlyfailedwiththeexceptionoftoolsthatcanidentifymicroRNAs. Methodology/Principal Findings: We present a very general ab initio ncRNA gene finder that exploits differential distributionsofsequencemotifsbetweenncRNAsandbackgroundgenomesequences. Conclusions/Significance:Ourmethod,oncetrainedonasetofncRNAsfromagivenspecies,canbeappliedtoagenome sequences of other organisms to find not only ncRNAs homologous to those in the training set but also others that potentiallybelongtonovel(andperhapsunknown)ncRNAfamilies.Availability:http://compbio.cs.sfu.ca/taverna/smyrna Citation:SalariR,AksayC,KarakocE,UnrauPJ,HajirasoulihaI,etal.(2009)smyRNA:ANovelAbInitioncRNAGeneFinder.PLoSONE4(5):e5433.doi:10.1371/ journal.pone.0005433 Editor:StefanMaas,LehighUniversity,UnitedStatesofAmerica ReceivedOctober12,2008;AcceptedMarch9,2009;PublishedMay5,2009 Copyright: ? 2009 Salari et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricteduse,distribution,andreproductioninanymedium,providedtheoriginalauthorandsourcearecredited. Funding:NSERC,CRCProgram,CFI,MITACS,andMSFHR:thefundershadnoroleinstudydesign,datacoll