AMD, an Automated Motif Discovery Tool Using Stepwise Refinement of Gapped Consensuses 英文参考文献.docVIP

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AMD, an Automated Motif Discovery Tool Using Stepwise Refinement of Gapped Consensuses 英文参考文献.doc

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AMD, an Automated Motif Discovery Tool Using Stepwise Refinement of Gapped Consensuses 英文参考文献

AMD,anAutomatedMotifDiscoveryToolUsing StepwiseRefinementofGappedConsensuses JiantaoShi1,3,WentaoYang2,MingjieChen2,YanzhiDu1,JiZhang1,2*,KankanWang2 1KeyLaboratoryofStemCellBiology,InstituteofHealthSciences,ShanghaiInstitutesforBiologicalSciences,ChineseAcademyofSciences,Shanghai,China,2Shanghai InstituteofHematologyandSino-FrenchCenterforLifeScienceandGenomics,Rui-JinHospitalaffiliatedtoShanghaiJiaoTongUniversitySchoolofMedicine,Shanghai, China,3GraduateSchooloftheChineseAcademyofSciences,Shanghai,China Abstract Motifdiscoveryisessentialfordecipheringregulatorycodesfromhighthroughputgenomicdata,suchasthosefromChIP- chip/seqexperiments.However,thereremainsalackofeffectiveandefficientmethodsfortheidentificationoflongand gapped motifs in many relevant tools reported to date. We describe here an automated tool that allows for de novo discoveryoftranscriptionfactorbindingsites,regardlessofwhetherthemotifsarelongorshort,gappedorcontiguous. Citation:ShiJ,YangW,ChenM,DuY,ZhangJ,etal.(2011)AMD,anAutomatedMotifDiscoveryToolUsingStepwiseRefinementofGappedConsensuses.PLoS ONE6(9):e24576.doi:10.1371/journal.pone.0024576 Editor:AshokAiyar,LouisianaStateUniversityHealthSciencesCenter,UnitedStatesofAmerica ReceivedApril4,2011;AcceptedAugust14,2011;PublishedSeptember12,2011 Copyright:?2011Shietal.Thisisanopen-accessarticledistributedunderthetermsoftheCreativeCommonsAttributionLicense,whichpermitsunrestricted use,distribution,andreproductioninanymedium,providedtheoriginalauthorandsourcearecredited. Funding:ThisworkwassupportedinpartbygrantsfromMinistryofScienceandTechnologyofChina(2009CB825607and2011CB910202),theNationalNatural Science Foundation and, Chinese Academy of Sciences (KSCX1-YW-22-01) and the Shanghai Commission of Science and Technology (09410706500).Thefundershadnoroleinstudydesign,datacollectionandanalysis,decisiontopublish,orpreparationofthemanuscript. CompetingInterests:Theauthorshavedeclaredthatnocompetinginterestsexist. *E-mail:jizhang@ Intro