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植物分子生物学网站GRAMENE-ppt介绍.ppt
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1、AComparativeGenomicMappingResourceforGrainsGrameneisacurated,open-source,Web-accessibledataresourceforcomparativegenomeanalysisinthegrasses.Asaninformationresource,Gramenespurposeistoprovideaddedvaluetodatasetsavailablewithinthepublicsectortofacilitateresearchersabilitytoleveragethericegenomicsequen
2、cetoidentifyandunderstandcorrespondinggenes,pathwaysandphenotypesinthecropgrasses.Thisisachievedbybuildingautomatedandcuratedrelationshipsbetweenriceandothercerealsforbothsequenceandbiology.Extensiveworkoverthepasttwodecadeshasshownremarkablyconsistentconservationofgeneorderwithinlargesegmentsoflink
3、agegroupsinrice,maize,sorghum,barley,wheat,rye,sugarcaneandotheragriculturallyimportantgrasses.Asubstantialbodyofdatasupportsthenotionthatthericegenomeissignificantlycolinearatbothlargeandshortscaleswithothercropgrasses,openingthepossibilityofusingricesyntenyrelationshipstorapidlyisolateandcharacter
4、izehomologuesinmaize,wheat,barleyandsorghum.Gramene ModulesThebestplacetobeginasearchatGrameneisofteninthemoduleofwhatyouwant.Ifyouwantinformationonamarker,lookinthemarkersmodule,ifyouwanttolearnaboutaprotein,gototheproteinsmodule.AnothergoodplacetostartiswiththeQuickSearchonthehomepage,alsofoundatt
5、hetoprightofallotherpages.Eventually,youwillfindthatmostofthemodulesareinterconnected,andyoumaymovebetweenmodulesasyoursearchprogresses.www.gramene.orgAccessGramenemodulesthroughtheNavigationbar.Thisisthelistofcurrentmodulesavailable.NoteThepresentationofthemodulesisorganizedaccordingtotheirlocation
6、onthenavigationbar.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
7、 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
8、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
9、 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 Vie
10、wFeaturesESTsGSSsFSTsArraysMarkersDecorationsExportJump ToWidthIdentifythelocationofaparticulargene,trait,QTLormarker-andthegrassspeciestheyhavebeenmappedto-ongenetic,QTL,physical,sequence,anddeletionmaps.UsetheCMapviewertoexaminetheco-linearityofaparticularregioninonechromosomeorspeciestoanother;or
11、inferwhichlinkagegroupinonespeciesismostconservedwithalinkagegroupinanotherspecies.Determinewhichmapsarethebestformakingcomparisons.Maps and CMapCompare Maps and Customize OptionsThe two images here reflect the same map comparison with different options selected for display.Locateaspecificmarkerbase
12、duponname,typeorspecies.Viewmarkerinformation,includingID,germplasmandgenomepositioning.Getmarker-typespecificinformation.LinktotheMaps,LiteratureandOntologiesDatabases.Markers DatabaseMarker Search MapMarkersMarker NameSynonymsSpeciesMarker TypeGR_TaxOntologiesLiteratureOther DBMapsSearchMarkerIDMa
13、rkerNameSynonymsMarkerTypeSpeciesGermplasmLibraryDescriptionMappingsCorrespondencesCloneRepeatMotifForwardPrimerReversePrimerAnnealTemperatureExpectedPCRProductSizeRemarksSequenceSourceGenomePositionsDBcross-referencesImagesOntologies SearchOntology AccessionAspect(Ontology)SynonymsDefinitionOntolog
14、yTermAspectDefinitionExternal ReferencesDerivationAnnotationsOntology Term NameObjectObject AccessionObject SymbolObject NameObject SynonymObject SpeciesEvidenceLiterature DBGenomes DBMaps DBProteins DBGenes DBQTL DBMarker DBOntologies MapSearchProtein accessionNames/Symbols/SynonymsOrganism(Cultiva
15、r)Evidence CodesProtein NameSymbolSynonymEC#Gene NameLink to BLASTGen Bank AccessionTrembl AccessionSpecies&CultivarPhenotypeCommentOntology AssociationsReferencesEvidence CodesProtein SimilaritiesProtein FeaturesFASTA sequenceGramene BLAST BrowseOntology DBAssociated ProteinsOntologies DBNCBI,E
16、xPaSy,GRINIRIS,PFam,.PROSITE,ProtomapLiterature DBGenes DBDetailed Information from Proteins DatabaseQTL DatabaseQTL(QuantitativeTraitLoci)areastatisticalcreationthatidentifiesaparticularregionofthegenomeascontainingagene(orgenes)thatisassociatedwiththetraitbeingassayedormeasured.Learnwhichtraitisas
17、sociatedwithaQTL,findwhereitislocatedonamap,andconstructcomparisonswithothermaps.DeterminewhichmarkersdelimitaQTLDeterminewhatgenesarelocatedinthesameregionasothergenesTrait CategoriesTraits at Gramene are categorized according to:Abiotic stress:Traitsrelatedtostressesfromabioticenvironment,e.g.,wat
18、er,light,temperature,orchemical.Anatomy:Traitsdirectlymeasuringplantpartssuchasroot,stemorleaf.Biochemical:Biochemicalandphysiologicaltraits,e.g.,enzymeactivity.Biotic stress:Traitsrelatedtostressesfrompestsandpathogens.Development:Traitsrelatedtoplantandplantpartdevelopment.Alsoincludesmaturityrela
19、tedtraits.Quality:Traitsofeconomicimportancethatmayaffectproductquality.Sterility or fertility:Traitsrelatedtomaleandfemaleflowersterilityorfertility,includingincompatibility.Vigor:Traitsrelatedtogrowthanddormancy.Yield:Traitscontributingdirectlytoyieldbasedoneconomicvalue.Browse TraitsTrait NameTra
20、it SymbolTO Accession#of QTLSpecies NameTrait NameTrait SynonymsLinkage GroupTrait CategoryTrait symbolPublished SymbolQTL AccessionMap set nameMap PositionQTL AccessionSpeciesPublished SymbolTrait SymbolTrait NameTO AccessionTrait SynonymsTrait CategoryLinkage GroupMap PositionGenome PositionCommen
21、tsDBX ReferencesQTL SearchMaps DBLiterature DBOntology DBGenomes DB1123QTL Data MapDiversitySearchbyGermplasmPassport DataAccessiondataSynonymsHoldingInstituteStockSourceGermplasmTaxonomydtaCollection DataCollector,LocationExperiment DataTitleDesignPolymorphismtypeScoringProtocolProducerOriginatorCo
22、mmentsAlleledataMarker and Allele DataAccession#AccessionnameLocusnameGenotypeAllgenotypesonamarker/germplasmsSearchbyMarkerLiteratureDBMarkersDBExternalgermplasmDBsDiversity Data MapRetrievedescriptionsofallelesassociatedwithmorphological,developmental,andagronomicallyimportantphenotypesandvariants
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