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Flagdb++ a database for the functional analysis of the arabidopsis genome. Nucleic Acids Re

NucleicAcidsResearch,2004,Vol.32,DatabaseissueD347±D350

DOI:10.1093/nar/gkh134

FLAGdb++:adatabaseforthefunctionalanalysisoftheArabidopsisgenome

ÂroniqueBrunaud,SylvainDucheÃne,YannickDeOliveira,FranckSamson,Ve

ÂbastienAubourg*MichelCaboche,AlainLecharnyandSe

ÂdeRechercheenGeÂnomiqueVeÂgeÂtale(URGV),UMRINRA1165,CNRS8114,UniversiteÂd'EvryValUnite

Âmieux,CP5708,F-91057EvryCedex,Franced'Essonne,2rueGastonCre

ReceivedAugust12,2003;RevisedOctober16,2003;AcceptedOctober27,2003

ABSTRACT

FLAGdb++isdedicatedtotheintegrationandvisual-izationofdataforhigh-throughputfunctionalanaly-sisofafullysequencedgenome,asillustratedfor

Arabidopsis.FLAGdb++displaysthepredictedorexperimentaldatainaposition-dependentwayanddisplayscorrelationsandrelationshipsbetweendifferentfeatures.FLAGdb++providesforagivengenomeregion,summarizedcharacteristicsofexperimentalmaterialslikeprobelengths,locationsandspeci®citieshavinganimpactuponthecon-®dencewewillputintheexperimentalresults.Aselectedsubsetoftheavailableinformationislinkedtoalocusrepresentedonaneasy-to-interpretandmemorablegraphicaldisplay.Dataarecurated,processedandformattedbeforetheirintegrationintoFLAGdb++.FLAGdb++containsdifferentoptionsforeasybackandforthnavigationthroughmanylociselectedatthestartofasession.Itincludesanoriginaltwo-componentvisualizationofthedata,agenome-wideandalocalview,whichareperman-entlylinkedanddisplaycomplementaryinforma-tion.Densitycurvesalongthechromosomesmaybedisplayedinparallelforsuggestingcorrelationsbetweendifferentstructuralandfunctionaldata.FLAGdb++isfullyaccessibleathttp://www.51wendang.combiogen.fr/FLAGdb/.INTRODUCTION

Sequencingprojectsprovideputativegenesarrayedalonglinearorcircularrepresentationsofchromosomes.Thus,insomedatabases,thevisualizationofgenesisbasedona1Ddisplayofgeneneighbourhood[e.g.forArabidopsis,TAIR(1)andtheGMOD-AtIDBproject(2)].Neverthelessthegenecontextisfarfrombeinglimitedtoneighbouringregionsandofteninvolveselementslocatedondifferentchromosomes.WithFLAGdb++weintendtoexplorefurtherthepotentialitiesofa1Dtopologicalrepresentationanditsuseforhigh-throughput(HTP)functionalanalysisoftheArabidopsis

genome.Insilicofunctionalannotationismainlyaprocessofnavigationthroughvariousdatabasesfollowedbyasynthesisofallretrievedinformation.Muchasgenomesequenceannotatorsdesireddedicatedgraphicaltools,suchasARTEMIS(3),HTPfunctionalgenomicistsneedwarehousedatabaseswithgraphicaldisplaysthataidnavigationandinformationsynthesis.FLAGdb++isbeingdevelopedtohelpanalysisofrawdatafromdifferentHTPfunctionalapproachessuchasmassivesequencingofT-DNAmutants,genome-widecharacterizationofgenefamiliesandtranscriptomestudies.Selected,valued,quality-labelledandeventuallyweigheddatathatarethoughttobeofdirectinterestforfunctionalanalysesareprogressivelylayeredontothesamedatabaseschemeunderlainbythesequencesofthe®veArabidopsischromosomes(4).

TECHNICALDESCRIPTIONOFTHEDATABASEFLAGdb++hasbeenimplementedintheRelationalDatabaseManagementSystemORACLEv8.i.Thedatabasearchitec-turetomanagethedataaroundthegenomicsequencesisbasedonthepreviouslyconstructedMICADO(5)andFLAGdb/FST(6)databases.AllthegraphicalinterfacesaredevelopedwithJAVAJDK1.4.JAVAWEBSTARTtechnologyisusedtofacilitateFLAGdb++installationandtheautomaticupgradeofnewreleases.Theconnectivitybetweenthelocallyinstalledapplicationandthedatabaseisbuiltonclient-serverarchitectureusingJDBCprotocols.DatacontentofFLAGdb++

ThegeneralconceptofFLAGdb++istheanchoringofdifferentkindsofdatatogenomicsequences,eithercompletechromosomesorsequencedBACclones.Integrateddataareofaheterogeneousnaturebutarealldescribedbyatleastacoordinatesetrelativetoagenomicsequence.Dataareselectedandcuratedasafunctionoftheirinterestforfunctionalanalysis.Theycanbetheresultofexperimentalworkorgeneratedbybioinformaticspredictionsoftware.Figure1describesthedataintegratedintotheversion1.4ofFLAGdb++.Thegeneralideaistokeepthedifferentdataindependentasmuchaspossible.Thus,eachnovelpieceofdataismappedtothegenomicsequencesasanewfeatureindependentlyoftheotherfeaturesinordertoavoidtransitive

*Towhomcorrespondenceshouldbeaddressed.Tel:+33160874516;Fax:+33160874549;Email:aubourg@evry.inra.frTheauthorswishittobeknownthat,intheiropinion,the®rsttwoauthorsshouldberegardedasjointFirstAuthors

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