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1、AFieldGuidepart2 GenomeresourcesSequencesimilarity Apr 2007 ShandongUniversity GenomeResources LocusLink Genedatabase UniGene TraceArchive MapViewer Homologene GenomicBiology GenomeProjects microb GenomeResources LocusLink Genedatabase UniGene TraceArchive MapViewer Homologene Asinglequeryinterfacet
2、o Sequences RefSeqs GenBank HomologeneMaps MapViewerEntrezlinks LocusLink LocusLinkwillbereplacedbyEntrezGeneonMARCH1 2005 CheckGeneFAQforcurrentinformation EntrezGene LocusLink Asinglequeryinterfaceto Sequences RefSeqs GenBank HomologeneMaps MapViewerEntrezlinks EntrezGene Moreorganisms allRefSeqge
3、nomesEntrezintegration Gsn sym 淀粉样变性病 GlobalEntrez NADH2 nadh2 47 EntrezGene NADH2 26records GeneRecordforPongoNADH2 DisplayExons Introns GeneTable GeneTable ARecordWithMoreData HumanHFE 血色沉着病 GeneGraphicLinks Introns Exons GeneTable linkstosequence ARecordWithMoreData HumanHFE EntrezSNP hfe genenam
4、e ANDhuman orgn 52 血色沉着病 LinkingtoSNP 染色体定位 基因定位 序列定位 SNPinStructure LinktoOMIM VariantsinOMIM GenomeResources LocusLink Genedatabase TraceArchive MapViewer Homologene UniGene Gene orientedclustersofexpressedsequences AutomaticclusteringusingMegaBlastEachclusterrepresentsauniquegeneInformedbygenomeh
5、itsInformationontissuetypesandmaplocationsUsefulforgenediscoveryandselectionofmappingreagents UniGene AClusterofESTs query 5 ESThits 3 ESThits Unigene UniGeneCollections ExampleUniGeneCluster HistogramofclustersizesforUniGeneHsbuild177 UniGeneClusterHs 95351 UniGeneClusterHs 95351 UniGeneClusterHs 9
6、5351 expression UniGeneClusterHs 95351 seqs Downloadsequences webpage GenomeResources LocusLink Genedatabase UniGene TraceArchive MapViewer Homologene TheNewHomologene Automateddetectionofhomologsamongtheannotatedgenesofcompletelysequencedeukaryoticgenomes NolongerUniGenebasedProteinsimilaritiesfirs
7、tGuidedbytaxonomictreeIncludesorthologsandparalogs Orthologs和Paralogs是同源序列的两种类型 Orthologs 垂直同源基因 是指来自于不同物种的由垂直家系 物种形成 进化而来的蛋白 并且典型的保留与原始蛋白有相同的功能 Paralogs 平行同源基因 是那些在一定物种中的来源于基因复制的蛋白 可能会进化出新的与原来有关的功能 请参考文献获得更多的信息 geneduplication ParalogsvsOrthologs earlyglobingene A chaingeneB chaingene paralogs orth
8、ologsorthologs TheNewHomologene RAG1 Homologene rag1 12 recombinationactivatinggene RAG1 Homolgene RAG1 Amniota Homolgene RAG1 Homolgene RAG1 GenomeResources LocusLink Genedatabase UniGene TraceArchive MapViewer Homologene MapViewer ListView HumanMapViewer 腺甙脱氨酶 MapViewer HumanADAR 4 MVHsADAR Maps O
9、ptions Sequencemaps AbinitioAssemblyRepeatsBES CloneCloneNCI CloneContigComponentCpGislanddbSNPhaplotypeFosmidGenBank DNAGenePhenotypeSAGE TagSTSTCAG RNATranscript RNA Hs UniGeneHs EST Cytogeneticmaps IdeogramFISHCloneGene CytogeneticMitelmanBreakpointMorbid Disease GeneticMaps deCODEGenethonMarshfi
10、eld RHmaps GeneMap99 G3GeneMap99 GB4NCBIRHStandford G3TNGWhitehead RHWhitehead YAC Mm UniGeneMm ESTRn UniGeneRn ESTSsc UniGeneSsc ESTBt UniGeneBt ESTGga UniGeneGga ESTVariation Maps Options MapViewer UniGene Component Repeats Gene Mastermap repeats Gene Phenotype Variation Maps Options Maps Options
11、GenomeResources LocusLink Genedatabase UniGene TraceArchive MapViewer Homologene StrongylocentrotuspurpuratusTraces BLAST BasicLocalAlignmentSearchTool WebAccess BLAST VAST Entrez Text Sequence Structure BasicLocalAlignmentSearchTool Whyusesequencesimilarity BLASTalgorithmBLASTstatisticsBLASToutputE
12、xamples WhyDoWeNeedSequenceSimilaritySearching ToidentifyandannotatesequencesToevaluateevolutionaryrelationshipsOther modelgenomicstructure e g Spidey checkprimerspecificityinsilico NCBI stool BLASTWebsiteStats GlobalvsLocalAlignment GlobalvsLocalAlignment Seq1 WHEREISWALTERNOW 16aa Seq2 HEWASHEREBU
13、TNOWISHERE 21aa TheFlavorsofBLAST StandardBLASTtraditional contiguous wordhitpositionindependentscoringnucleotide proteinandtranslations blastn blastp blastx tblastn tblastx MegablastoptimizedforlargebatchsearchescanusediscontiguouswordsPSI BLASTconstructsPSSMsautomatically usesasqueryverysensitivep
14、roteinsearchRPSBLASTsearchesadatabaseofPSSMstoolforconserveddomainsearches WidelyusedsimilaritysearchtoolHeuristicapproachbasedonSmithWatermanalgorithmFindsbestlocalalignmentsProvidesstatisticalsignificanceAllcombinations DNA Protein queryanddatabase DNAvsDNA blastnDNAtranslationvsProtein blastxProt
15、einvsProtein blastpProteinvsDNAtranslation tblastnDNAtranslationvsDNAtranslation tblastxwww standalone andnetworkclients BasicLocalAlignmentSearchTool TranslatedBLAST Query Database Program ucleotide rotein N N N N P P blastx tblastn tblastx Particularlyusefulfornucleotidesequenceswithoutproteinanno
16、tations suchasESTsorgenomicDNA HowBLASTWorks Makelookuptableof words forqueryScandatabaseforhitsUngappedextensionsofhits initialHSPs Gappedextensions notraceback Gappedextensions traceback alignmentdetails NucleotideWords GTACTGGACATTACTGGACATGACTGGACATGGCTGGACATGGATGGACATGGACGGACATGGACCGACATGGACCCACATGGACCCT Makealookuptableofwords ProteinWords GTQTQIQITITVTVEVEDEDLDLF Makealookuptableofwords f11 blastpdefault MinimumRequirementsforaHit NucleotideBLASTrequiresoneexactmatchProteinBLASTrequirestw
