植物分子生物学网站GRAMENE-ppt介绍.ppt

uencetoidentifyandunderstandcorrespondinggenes,pathwaysandphenotypesinthecropgrasses.Thisisachievedbybuildingautomatedandcuratedrelationshipsbetweenriceandothercerealsforbothsequenceandbiology.Extensiveworkoverthepasttwodecadeshasshownremarkablyconsistentconservationofgeneorderwithinlargesegmentsoflinkagegroupsinrice,maize,sorghum,barley,wheat,rye,sugarcaneandotheragriculturallyimportantgrasses.Asubstantialbodyofdatasupportsthenotionthatthericegenomeissignificantlycolinearatbothlargeandshortscaleswithothercropgrasses,openingthepossibilityofusingricesyntenyrelationshipstorapidlyisolateandcharacterizehomologuesinmaize,wheat,barleyandsorghum.Gramene ModulesThebestplacetobeginasearchatGrameneisofteninthemoduleofwhatyouwant.Ifyouwantinformationonamarker,lookinthemarkersmodule,ifyouwanttolearnaboutaprotein,gototheproteinsmodule.AnothergoodplacetostartiswiththeQuickSearchonthehomepage,alsofoundatthetoprightofallotherpages.Eventually,youwillfindthatmostofthemodulesareinterconnected,andyoumaymovebetweenmodulesasyoursearchprogresses.www.gramene.orgAccessGramenemodulesthroughtheNavigationbar.Thisisthelistofcurrentmodulesavailable.NoteThepresentationofthemodulesisorganizedaccordingtotheirlocationonthenavigationbar.Thisdoesnotindicatethatyoushouldbeginwiththefirstmodulepresented,norendwiththelastone.TogetherthemodulescomplementeachotherbyformingtheGrameneDatabase.Genome browser is a dynamic graphical display used to browse genomes.Use it to:Search for genes and other features identified from the Rice-Japonica,Maize and Arabidopsis genomes,as well as features from maize,sorghum,barley and wheat that were mapped on the rice genome.View the location of a particular feature on the rice genomeExamine neighboring genes and markers.View the gene model of a candidate gene of interest in order to design primers.Identify the genomic sequence to which a particular gene is mapped.Look for synteny.Compare the position of features from other species with the location of genes in the rice genome,such as sequenced genetic markers,ESTs,cDNAs,CDSs,genes,insertion and repeat elements.Gramene Genome BrowserAugust2005Link to maps and ontologies from the genome browser.Upload your data to view in a karyotype ideogram.Download genetic information Customize your results specifically for the information you need.Genome BrowserBrowse a Chromosome or View a Synteny MapCustomize options for Contig ViewFeaturesESTsGSSsFSTsArraysMarkersDecorationsExportJump ToWidthIdentifythelocationofaparticulargene,trait,QTLormarker-andthegrassspeciestheyhavebeenmappedto-ongenetic,QTL,physical,sequence,anddeletionmaps.UsetheCMapviewertoexaminetheco-linearityofaparticularregioninonechromosomeorspeciestoanotherorinferwhichlinkagegroupinonespeciesismostconservedwithalinkagegroupinanotherspecies.Determinewhichmapsarethebestformakingcomparisons.Maps and CMapCompare Maps and Customize OptionsThe two images here reflect the same map comparison with different options selected for display.Locateaspecificmarkerbaseduponname,typeorspecies.Viewmarkerinformation,includingID,germplasmandgenomepositioning.Getmarker-typespecificinformation.LinktotheMaps,LiteratureandOntologiesDatabases.Markers DatabaseMarker Search MapMarkersMarker NameSynonymsSpeciesMarker TypeGR_TaxOntologiesLiteratureOther DBMapsSearchMarkerIDMarkerNameSynonymsMarkerTypeSpeciesGermplasmLibraryDescriptionMappingsCorrespondencesCloneRepeatMotifForwardPrimerReversePrimerAnnealTemperatureExpectedPCRProductSizeRemarksSequenceSourceGenomePositionsDBcross-referencesImagesOntologies SearchOntology AccessionAspect(Ontology)SynonymsDefinitionOntologyTermAspectDefinitionExternal ReferencesDerivationAnnotationsOntology Term NameObjectObject AccessionObject SymbolObject NameObject SynonymObject SpeciesEvidenceLiterature DBGenomes DBMaps DBProteins DBGenes DBQTL DBMarker DBOntologies MapSearchProtein accessionNames/Symbols/SynonymsOrganism(Cultivar)Evidence CodesProtein NameSymbolSynonymEC#Gene NameLink to BLASTGen Bank AccessionTrembl AccessionSpecies&CultivarPhenotypeCommentOntology AssociationsReferencesEvidence CodesProtein SimilaritiesProtein FeaturesFASTA sequenceGramene BLAST BrowseOntology DBAssociated ProteinsOntologies DBNCBI,ExPaSy,GRINIRIS,PFam,.PROSITE,ProtomapLiterature DBGenes DBDetailed Information from Proteins DatabaseQTL DatabaseQTL(QuantitativeTraitLoci)areastatisticalcreationthatidentifiesaparticularregionofthegenomeascontainingagene(orgenes)thatisassociatedwiththetraitbeingassayedormeasured.LearnwhichtraitisassociatedwithaQTL,findwhereitislocatedonamap,andconstructcomparisonswithothermaps.DeterminewhichmarkersdelimitaQTLDeterminewhatgenesarelocatedinthesameregionasothergenesTrait CategoriesTraits at Gramene are categorized according to:Abiotic stress:Traitsrelatedtostressesfromabioticenvironment,e.g.,water,light,temperature,orchemical.Anatomy:Traitsdirectlymeasuringplantpartssuchasroot,stemorleaf.Biochemical:Biochemicalandphysiologicaltraits,e.g.,enzymeactivity.Biotic stress:Traitsrelatedtostressesfrompestsandpathogens.Development:Traitsrelatedtoplantandplantpartdevelopment.Alsoincludesmaturityrelatedtraits.Quality:Traitsofeconomicimportancethatmayaffectproductquality.Sterility or fertility:Traitsrelatedtomaleandfemaleflowersterilityorfertility,includingincompatibility.Vigor:Traitsrelatedtogrowthanddormancy.Yield:Traitscontributingdirectlytoyieldbasedoneconomicvalue.Browse TraitsTrait NameTrait SymbolTO Accession#of QTLSpecies NameTrait NameTrait SynonymsLinkage GroupTrait CategoryTrait symbolPublished SymbolQTL AccessionMap set nameMap PositionQTL AccessionSpeciesPublished SymbolTrait SymbolTrait NameTO AccessionTrait SynonymsTrait CategoryLinkage GroupMap PositionGenome PositionCommentsDBX ReferencesQTL SearchMaps DBLiterature DBOntology DBGenomes DB1123QTL Data MapDiversitySearchbyGermplasmPassport DataAccessiondataSynonymsHoldingInstituteStockSourceGermplasmTaxonomydtaCollection DataCollector,LocationExperiment DataTitleDesignPolymorphismtypeScoringProtocolProducerOriginatorCommentsAlleledataMarker and Allele DataAccession#AccessionnameLocusnameGenotypeAllgenotypesonamarker/germplasmsSearchbyMarkerLiteratureDBMarkersDBExternalgermplasmDBsDiversity Data MapRetrievedescriptionsofallelesassociatedwithmorphological,developmental,andagronomicallyimportantphenotypesandvariantsofphysiologicalcharacters,biochemicalfunctionsandisozymes.Getagenesinformation,includinginformationonnameofthegene,genesymbol,relatedphenotypes(traits),images,alleleandgermplasm.LinktoLiteratureandOntologydatabases.Viewassociatedmapsandsequencingdata.Gene&Allele DatabaseClickathumbnailtoenlargeimage.Selectdesireddetailedinfofrommenuandclick.Gene Detail Page Gene Data MapGene SymbolGene NameChromosomeSpeciesGene TypeOntology AssociationsSynonymsGene AccessionGene SymbolGene NameSynonymsSpeciesChromosomeGene TypeHas Phenotype?DescriptionPhenotypic imageCurator CommentsAlleleGermplasmSequence AssociationMapReferencesAllele AccessionAllele SymbolAllele NameDescriptionAllelic interactionStudyGermplasmGene nameOntology AssociationsStudy NameYearSeasonStudy LocationStudy TypeEnvironmental FactorsAllelesReferences Germplasm AccessionLocationWildtypeMutagenMutagenesis MethodGeneProteinNucleotide(DNA)Map set nameChromosomePositionsProtein DBMaps DBGenBank(NCBI)Literature DBGenomes DBOntologyDatabaseGene SearchOryzabaseMaizeGDBGene InformationGene SymbolGene NameChromosomeSpeciesGene TypeOntology AssociationsSynonymsGene AccessionGene SymbolGene NameSynonymsSpeciesChromosomeGene TypeHas Phenotype?DescriptionPhenotypic imageCurator CommentsAlleleGermplasmSequence AssociationMapReferencesAllele AccessionAllele SymbolAllele NameDescriptionAllelic interactionStudyGermplasmGene nameOntology AssociationsStudy NameYearSeasonStudy LocationStudy TypeEnvironmental FactorsAllelesReferences Germplasm AccessionLocationWildtypeMutagenMutagenesis MethodGeneProteinNucleotide(DNA)Map set nameChromosomePositionsProtein DBMaps DBGenBank(NCBI)Literature DBGenomes DBOntologyDatabaseGene SearchOryzabaseMaizeGDBProteins DatabaseProvidescollectiveinformationonproteinsfromgrasses(familyPoaceae/Gramineae),andareannotatedaccordingtoGeneOntologyandPlantOntology.GeneOntology(GO)Molecularfunctionofthegeneproduct.Biologicalprocessinwhichthegeneproductisinvolved.Cellularcomponentwherethegeneproductislocalized.PlantOntologyPlantstructurewherethegeneisexpressed(PO)Plantgrowthstageatwhichthegeneisexpressed(GRO)*Only rice(Oryza)protein entries are manually curated.FindaproteinandconductaBLASTqueryonit.Determinethemolecularfunction,biologicalprocessorcellularlocationofaparticularriceprotein.Findproteinsequenceinformationandorthologsfromotherspecies.Findwhichproteinsaremembersofaproteinfamily(Pfam&PROSITE).Linktoontologyandliteraturedatabases.ProteinsGeneral Protein InfoA textual description of the proteinProtein Detail Page:General InformationCross references to GenBank and SWISSPROT protein entries.Selectinformationofinteresttoyou.SearchProtein accessionNames/Symbols/SynonymsOrganism(Cultivar)Evidence CodesProtein NameSymbolSynonymEC#Gene NameLink to BLASTGen Bank AccessionTrembl AccessionSpecies&CultivarPhenotypeCommentOntology AssociationsReferencesEvidence CodesProtein SimilaritiesProtein FeaturesFASTA sequenceGramene BLAST BrowseOntology DBAssociated ProteinsOntologies DBNCBI,ExPaSy,GRINIRIS,PFam,.PROSITE,ProtomapLiterature DBGenes DBProteins Data MapThisdatabaseisacollectiveresourceofstructuredcontrolledvocabularies(Ontologies)forknowledgedomainsandtheirassociations.PlantOntology(PO)PlantStructure(morphology,organs,tissueandcelltypes)*Growthstages(plantgrowthanddevelopmentalstages)(GRO)TraitOntology(TO)PlanttraitsandphenotypesGeneOntology(GO)MolecularfunctionBiologicalprocessCellularcomponentEnvironmentOntology(EO)Gramenestaxonomyontology(GR_tax)Associations:FindEnsemblricegenes(fromTIGRsricegenomeassembly),proteinsfromSWISSPROT-TrEMBLrepresentingPoaceae(grass)family,ricegenes,QTLandmapsets.OntologiesNote:Remember that different ontologies are for different purposes and do not overlap with each other.For more information on each ontology type please visit the current ontologies section at Gramene OntologiesUsingontologieswillassistusersintheirsearches.AnOntologyisaglossaryofkeywordsarrangedinastructuredorder/networkbasedonthebiologicalconceptthatdescribesthekeywordsrelationshipinanontologytree.Researchersareworkingtowardsastandardizedontology,thusfacilitatingsearchingindifferentdatabases.The lineage of alpha-amylase activity as a molecular functionTerm-term relationshipi:IS A(type of)Number of database objects associated in the database with this term.Exact ontology termDefinition of the termOntology Term Accession DetailOntologies SearchOntology AccessionAspect(Ontology)SynonymsDefinitionOntologyTermAspectDefinitionExternal ReferencesDerivationAnnotationsOntology Term NameObjectObject AccessionObject SymbolObject NameObject SynonymObject SpeciesEvidenceLiterature DBGenomes DBMaps DBProteins DBGenes DBQTL DBMarker DBOntologies Data MapPathways(RiceCyc)RiceCycallowsbiochemicalpathwaystobeanalyzedandvisualized.ThistutorialhasbeendevelopedforfirsttimeandcasualusersofRiceCyc.ToaccessamoredetailedoverviewoftheprogramsfeaturesandthedatacontainedwithinpleaserefertothePathwayslinksavailablefromthePathwayshomepage.FormoreinformationonPathwaystools,seehere.RiceCyc allows biochemical pathways to be analyzedandvisualized.GramenehasincorporatedthelatestTIGR4genomeintothis release to create an Oryza sativa specific pathwaydataset.Dataisunderdevelopmentandsubjecttochange.IfyoudoseeanyerrorsinthedatasetpleasefeelfreetocontactusthroughthefeedbackprovidedatthetopofGramenewebpages.IntroductionTheflowofthepathwayisfromthetopofthepagetothebottomBiosyntheticpathwaysTCACycleCatabolicOrphanMetabolic Map Overview Level4Pathway DetailLevel5Movebetweenlevelswith“moredetail”and“lessdetail”buttons.LiteraturesearchesareagoodoptionforbeginningyourGramenesearch.Searchforcitationsonrice,aswellasotherspecies.LiteraturesearchresultsprovidelinkstopublicationsourcesandotherGramenedatabaseswhereavailable.LiteratureLiteratureFindarticlesaboutgenes,proteins,QTL,markers,orontology.Linktomapsdescribedinthegivencitations,aswellasthegene,QTL,proteinandmarkerdatabases.Literature DetailClickheretolinktocross-referenced resources.GramenesIDfor that referenceLiterature Data MapLiteratureRice Genetics NewsletterAuthorPublicationTitleAbstractReference IDCross ReferencesAssociated DataSource WebsiteQTLGenesMarkersProteinsMapsBLASTBLASTisatool.SearchforsequencesimilaritymatchesintheGramenedatabase.Selectthebesttargetdatabaseforyoursearch.Choosethebestalgorithmforyoursearch.Fine-tunesearchparameters.Displaymatchresults.August2005BLAST Data MapBLASTticket IDHigh Scoring PairsLocations vs.KaryotypeLocations vs QueryChromosomeStartStopCloneAlignmentSequenceGenomic SequenceContigviewRaw ScorePercent IDLengthP-valueE-valueGenome BrowserGrameneMartBatchDataSequenceRetrievalSelectaGramenedatasettosearchagainst.Addfilterstothedatasettoincreaseitsspecificity.Choosethefieldstoincludeinthereport.Generateabatchreportinaformatthatcanbeimportedintolocaltools,suchasExcel.GrameneMartisbaseduponBiomart.Martisparticularlysuitedforprovidingthedatamininglikesearchesofcomplexdescriptive(e.g.biological)data,andisoptimizedforlargedatabases,suchasgenomicsequenceormicroarrayexperiments.BioMartsoftwareiscompletelyOpenSource,licensedundertheLGPL,andfreelyavailabletoanyonewithoutrestrictions