PeanutDB an integrated bioinformatics web portal for Arachis hypogaea transcriptomics 英文参考文献.docVIP

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PeanutDB an integrated bioinformatics web portal for Arachis hypogaea transcriptomics 英文参考文献.doc

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PeanutDB an integrated bioinformatics web portal for Arachis hypogaea transcriptomics 英文参考文献

Duanetal.BMCPlantBiology2012,12:94 /1471-2229/12/94 DATABASE OpenAccess PeanutDB:anintegratedbioinformaticsweb portalforArachishypogaeatranscriptomics XiaohongDuan1,EmilySchmidt2,3,PeiLi2,DouglasLenox2,3,LinLiu2,ChanglongShu1,JieZhang1* andChunLiang2,3* Abstract Background:Thepeanut(Arachishypogaea)isanimportantcropcultivatedworldwideforoilproductionandfood sources.Itscomplexgeneticarchitecture(e.g.,thelargeandtetraploidgenomepossiblyduetouniquecrossofwild diploidrelativesandsubsequentchromosomeduplication:2n=4x=40,AABB,2800Mb)presentsamajorchallenge foritsgenomesequencingandmakesitaless-studiedcrop.Withoutadoubt,transcriptomesequencingisthe mosteffectivewaytoharnessthegenomestructureandgeneexpressiondynamicsofthisnon-modelspeciesthat hasalimitedgenomicresource. Description:Withthedevelopmentofnextgenerationsequencingtechnologiessuchas454pyro-sequencingand Illuminasequencingbysynthesis,thetranscriptomicsdataofpeanutisrapidlyaccumulatedinboththepublic databasesandprivatesectors.Integrating187,636Sangerreads(103,685,419bases),1,165,168Roche454reads (333,862,593bases)and57,135,995Illuminareads(4,073,740,115bases),wegeneratedthefirstreleaseofourpeanut transcriptomeassemblythatcontains32,619contigs.WeprovidedEC,KEGGandGOfunctionalannotationsto thesecontigsanddetectedSSRs,SNPsandothergeneticpolymorphismsforeachcontig.Basedonboth open-sourceandourin-housetools,PeanutDBpresentsmanyseamlesslyintegratedwebinterfacesthatallowusers tosearch,filter,navigateandvisualizeeasilythewholetranscriptassembly,itsannotationsanddetected polymorphismsandsimplesequencerepeats.Foreachcontig,sequencealignmentispresentedinbothbird’s-eye viewandnucleotidelevelresolution,withcolorfullyhighlightedregionsofmismatches,indelsandrepeatsthat facilitatecloseexaminationofassemblyquality,geneticpolymorphisms,sequencerepeatsand/or sequencingerrors. Conclusion:Asapublicgenomicdatabasethatintegratespeanuttranscriptomedatafromdifferentsources, PeanutDB(/txid3818v1)providesthePeanutresearchcommunitywithaneas