淀粉樣變性病講解課件

AFieldGuide

part2

GenomeresourcesSequencesimilarityApr,2007ShandongUniversityAFieldGuide

part2Genomer1GenomeResourcesLocusLinkGenedatabaseUniGeneTraceArchiveMapViewerHomologeneGenomeResourcesLocusLinkGene2GenomicBiologyGenomicBiology3淀粉樣變性病講解課件4淀粉樣變性病講解課件5淀粉樣變性病講解課件6GenomeProjects:microbGenomeProjects:microb7淀粉樣變性病講解課件8淀粉樣變性病講解課件9GenomeResourcesLocusLinkGenedatabaseUniGeneTraceArchiveMapViewerHomologeneGenomeResourcesLocusLinkGene10Asinglequeryinterfaceto…

Sequences -RefSeqs -GenBank -HomologeneMaps–MapViewerEntrezlinksLocusLinkLocusLinkwillbereplacedbyEntrezGeneonMARCH1,2005.CheckGeneFAQforcurrentinformation.Asinglequeryinterfaceto…

11EntrezGeneLocusLinkAsinglequeryinterfaceto…

Sequences-RefSeqs-GenBank-HomologeneMaps–MapViewer EntrezlinksEntrezGene

Moreorganisms-allRefSeqgenomesEntrezintegrationEntrezGeneLocusLinkAsingleq12Gsn[sym]淀粉樣變性病Gsn[sym]淀粉樣變性病13淀粉樣變性病講解課件14GlobalEntrez:NADH2nadh247GlobalEntrez:NADH2nadh24715EntrezGene:NADH226recordsEntrezGene:NADH226records16GeneRecordforPongoNADH2HomosapiensGeneRecordforPongoNADH2Hom17DisplayExons/Introns:GeneTableDisplayExons/Introns:GeneT18GeneTableGeneTable19ARecordWithMoreData:HumanHFE血色沉著病ARecordWithMoreData:Human20GeneGraphicLinksNM_NP_GeneGraphicLinksNM_NP_21Introns/Exons:GeneTablelinkstosequenceIntrons/Exons:GeneTablelin22ARecordWithMoreData:HumanHFEARecordWithMoreData:Human23EntrezSNPhfe[genename]ANDhuman[orgn]52血色沉著病EntrezSNPhfe[genename]ANDh24LinkingtoSNP染色體定位基因定位序列定位LinkingtoSNP染色體定位基因定位序列定位25SNPinStructureSNPinStructure26LinktoOMIMLinktoOMIM27VariantsinOMIMVariantsinOMIM28GenomeResourcesLocusLinkGenedatabaseTraceArchiveMapViewerHomologeneUniGeneGenomeResourcesLocusLinkGene29Gene-orientedclustersofexpressedsequences

AutomaticclusteringusingMegaBlastEachclusterrepresentsauniquegeneInformedbygenomehitsInformationontissuetypesandmaplocationsUsefulforgenediscoveryandselectionofmapping reagentsUniGeneGene-orientedclustersofexpr30AClusterofESTsquery5’ESThits3’ESThitsAClusterofESTsquery5’ESTh31UnigeneUnigene32UniGeneCollectionsUniGeneCollections33ExampleUniGeneClusterExampleUniGeneCluster34HistogramofclustersizesforUniGeneHsbuild177Histogramofclustersizesfor35UniGeneClusterHs.95351UniGeneClusterHs.9535136UniGeneClusterHs.95351UniGeneClusterHs.9535137UniGeneClusterHs.95351:expressionUniGeneClusterHs.95351:expr38UniGeneClusterHs.95351:seqsUniGeneClusterHs.95351:seqs39DownloadsequenceswebpageftpsiteDownloadsequenceswebpageftp40GenomeResourcesLocusLinkGenedatabaseUniGeneTraceArchiveMapViewerHomologeneGenomeResourcesLocusLinkGene41TheNewHomologeneAutomateddetectionofhomologsamongtheannotatedgenesofcompletelysequencedeukaryoticgenomes.NolongerUniGenebasedProteinsimilaritiesfirstGuidedbytaxonomictreeIncludesorthologsandparalogsTheNewHomologeneAutomatedde42

Orthologs和Paralogs是同源序列的兩種類型。

Orthologs（垂直同源基因）是指來自于不同物種的由垂直家系（物種形成）進(jìn)化而來的蛋白，并且典型的保留與原始蛋白有相同的功能。Paralogs（平行同源基因）是那些在一定物種中的來源于基因復(fù)制的蛋白，可能會進(jìn)化出新的與原來有關(guān)的功能。請參考文獻(xiàn)獲得更多的信息。Orthologs和Paralogs43geneduplicationParalogsvsOrthologsearlyglobingeneA-chaingene B-chaingenefrogAchickAmouseAmouse

BchickBfrogBparalogsorthologs

orthologsgeneduplicationParalogsvsOr44TheNewHomologene

HomologeneBuild37.2Species Numberofgenes inputgrouped groupsTheNewHomologene45RAG1→Homologenerag112recombinationactivatinggeneRAG1→Homologenerag112recombi46RAG1→HomolgeneRAG1AmniotaRAG1→HomolgeneRAG1Amniota47Homolgene:RAG1Homolgene:RAG148淀粉樣變性病講解課件49Homolgene:RAG1Homolgene:RAG150GenomeResourcesLocusLinkGenedatabaseUniGeneTraceArchiveMapViewerHomologeneGenomeResourcesLocusLinkGene51淀粉樣變性病講解課件52淀粉樣變性病講解課件53淀粉樣變性病講解課件54MapViewerMapViewer55ListViewListView56HumanMapVieweradar腺甙脫氨酶HumanMapVieweradar腺甙脫氨酶57MapViewer:HumanADAR4MapViewer:HumanADAR458MVHsADAR3’UTR5’UTRMVHsADAR3’UTR5’UTR59Maps&Options--Sequencemaps--AbinitioAssemblyRepeatsBES_CloneCloneNCI_CloneContigComponentCpGislanddbSNPhaplotypeFosmidGenBank_DNAGenePhenotypeSAGE_TagSTSTCAG_RNATranscript(RNA)Hs_UniGeneHs_EST--Cytogeneticmaps--IdeogramFISHCloneGene_CytogeneticMitelmanBreakpointMorbid/Disease--GeneticMaps--deCODEGenethonMarshfield--RHmaps--GeneMap99-G3GeneMap99-GB4NCBIRHStandford-G3TNGWhitehead-RHWhitehead-YACMm_UniGeneMm_ESTRn_UniGeneRn_ESTSsc_UniGeneSsc_ESTBt_UniGeneBt_ESTGga_UniGeneGga_ESTVariationMaps&Options=SNPMaps&Options--Sequencemaps-60MapViewerUniGeneComponentRepeatsGeneMapViewerUniGeneComponentRepea61Mastermap:repeatsMastermap:repeats62GenePhenotypeVariationGenePhenotypeVariation63Maps&OptionsMaps&OptionsMaps&OptionsMaps&Options64GenomeResourcesLocusLinkGenedatabaseUniGeneTraceArchiveMapViewerHomologeneGenomeResourcesLocusLinkGene65淀粉樣變性病講解課件66淀粉樣變性病講解課件67Strongylocentrotuspurpuratus

TracesStrongylocentrotuspurpuratus68BLASTBasicLocalAlignmentSearchToolBLASTBasicLocalAlignmentSea69WebAccessBLASTVASTEntrezTextSequenceStructureWebAccessBLASTVASTEntrezTextS70淀粉樣變性病講解課件71BasicLocalAlignmentSearchTool

Whyusesequencesimilarity?BLASTalgorithmBLASTstatisticsBLASToutputExamplesBasicLocalAlignmentSearchT72WhyDoWeNeed

SequenceSimilaritySearching?ToidentifyandannotatesequencesToevaluateevolutionaryrelationshipsOther:modelgenomicstructure(e.g.,Spidey)checkprimerspecificityinsilico:NCBI’stoolWhyDoWeNeed

SequenceSimil73BLASTWebsiteStatsBLASTWebsiteStats74GlobalvsLocalAlignmentSeq1Seq2Seq1Seq2GlobalalignmentLocalalignmentGlobalvsLocalAlignmentSeq175GlobalvsLocalAlignmentSeq1:WHEREISWALTERNOW(16aa)Seq2:HEWASHEREBUTNOWISHERE(21aa)GlobalSeq1: 1W--HEREISWALTERNOW16 WHERESeq2: 1HEWASHEREBUTNOWISHERE21LocalSeq1:1W--HERE5Seq1:1W--HERE5WHEREWHERESeq2:3WASHERE9Seq2:15WISHERE21GlobalvsLocalAlignmentSeq1:76TheFlavorsofBLASTStandardBLASTtraditional“contiguous”wordhitpositionindependentscoringnucleotide,proteinandtranslations(blastn,blastp,blastx,tblastn,tblastx)MegablastoptimizedforlargebatchsearchescanusediscontiguouswordsPSI-BLASTconstructsPSSMsautomatically;usesasqueryverysensitiveproteinsearchRPSBLASTsearchesadatabaseofPSSMstoolforconserveddomainsearchesTheFlavorsofBLASTStandardB77WidelyusedsimilaritysearchtoolHeuristicapproachbasedonSmithWatermanalgorithmFindsbestlocalalignmentsProvidesstatisticalsignificanceAllcombinations(DNA/Protein)queryanddatabase.DNAvsDNA

blastnDNAtranslationvsProtein

blastxProteinvsProtein

blastpProteinvsDNAtranslation

tblastnDNAtranslationvsDNAtranslation

tblastx

www,standalone,andnetworkclientsBasicLocalAlignmentSearchToolWidelyusedsimilaritysearch78TranslatedBLASTQueryDatabaseProgramNPucleotideroteinNNNNPPblastxtblastntblastxPPPPPPPPPPPPPPPPPPPPPPPPParticularlyusefulfornucleotidesequenceswithoutproteinannotations,suchasESTsorgenomicDNATranslatedBLASTQueryDatabaseP79HowBLASTWorksMakelookuptableof“words”forqueryScandatabaseforhitsUngappedextensionsofhits(initialHSPs)Gappedextensions(notraceback)Gappedextensions(traceback;alignmentdetails)HowBLASTWorksMakelookuptab80NucleotideWordsGTACTGGACATGGACCCTACAGGAAQuery:GTACTGGACATTACTGGACATGACTGGACATGGCTGGACATGGATGGACATGGACGGACATGGACCGACATGGACCCACATGGACCCTMakealookuptableofwords11-mer...828megablast711blastnminimumdefaultWORDSIZENucleotideWordsGTACTGGACATGGA81ProteinWordsGTQITVEDLFYNIATRRKALKNQuery:

NeighborhoodWordsLTV,MTV,ISV,LSV,etc.GTQTQIQITITVTVEVEDEDLDLF...MakealookuptableofwordsWordsize=3(default)Wordsizecanonlybe2or3[-f11=blastpdefault]ProteinWordsGTQITVEDLFYNIATRR82MinimumRequirementsforaHit

NucleotideBLASTrequiresoneexactmatchProteinBLASTrequirestwoneighboringmatcheswithin40aaGTQITVEDLFYNI

SEIYYNATCGCCATGCTTAATTGGGCTT

CATGCTTAATT

neighborhoodwordsoneexactmatchtwomatches[-A40=blastpdefault]MinimumRequirementsforaHit83BLASTPSummary

YLS

HFLSbjct287LEETYAKYLHKGASYFVYLSLNMSPEQLDVNVHPSKRIVHFLYDQEI333Query1IETVYAAYLPKNTHPFLYLSLEISPQNVDVNVHPTKHEVHFLHEESI47GappedextensionwithtracebackQuery1IETVYAAYLPKNTHPFLYLSLEISPQNVDVNVHPTKHEVHFLHEESI-LEV…50

+EYAYLKF+YLSL+SP++DVNVHP+KVHFL+++I++Sbjct287LEETYAKYLHKGASYFVYLSLNMSPEQLDVNVHPSKRIVHFLYDQEIATSI…337FinalHSP

+EYAYLKF+

L+SP++DVNVHP+KV

+++I

High-scoringpair(HSP)HFL18HFV15HFS14HWL13NFL13DFL12HWV10etc…YLS15YLT12

YVS12YIT10etc…NeighborhoodwordsNeighborhoodscorethresholdT(-f)=11Query:

IETVYAAYLPKNTHPFLYLSLEISPQNVDVNVHPTKHEVHFLHEESILEV…examplequerywordsBLASTPSummary84ScoringSystems-Nucleotides

AGCTA+1–3–3-3G–3+1–3-3C–3–3+1-3T–3–3–3+1IdentitymatrixCAGGTAGCAAGCTTGCATGTCA||||||||||||||||||| rawscore=19-9=10CACGTAGCAAGCTTG-GTGTCA[-r1-q-3]ScoringSystems-Nucleotides85ScoringSystems-ProteinsPositionIndependentMatricesPAMMatrices(PercentAcceptedMutation)Derivedfromobservation;smalldatasetof alignmentsImplicitmodelofevolutionAllcalculatedfromPAM1PAM250widelyusedBLOSUMMatrices(BLOckSUbstitutionMatrices)Derivedfromobservation;largedatasetofhighly conservedblocksEachmatrixderivedseparatelyfromblockswitha definedpercentidentitycutoffBLOSUM62-defaultmatrixforBLASTPositionSpecificScoreMatrices(PSSMs)

PSI-andRPS-BLASTScoringSystems-ProteinsPosi86A4R-15

N-206D-2-216C0-3-3-39Q-1100-35E-1002-425G0-20-1-3-2-26H-201-1-300-28I-1-3-3-3-1-3-3-4-34

L-1-2-3-4-1-2-3-4-324K-120-1-311-2-1-3-25M-1-1-2-3-10-2-3-212-15F-2-3-3-3-2-3-3-3-100-306P-1-2-2-1-3-1-1-2-2-3-3-1-2-47S1-110-1000-1-2-20-1-2-14T0-10-1-1-1-1-2-2-1-1-1-1-2-115W-3-3-4-4-2-2-3-2-2-3-2-3-11-4-3-211Y-2-2-2-3-2-1-2-32-1-1-2-13-3-2-227V0-3-3-3-1-2-2-3-331-21-1-2-20-3-14X0-1-1-1-2-1-1-1-1-1-1-1-1-1-200-2-1-1-1ARNDCQEGHILKMFPSTWYVXBLOSUM62DFNegativeforlesslikelysubstitutionsDYFPositiveformorelikelysubstitutionsA4BLOSUM62DFNegativeforles87Position-SpecificScoreMatrixDAF-1Serine/Threonineproteinkinasescatalyticloop174PSSMscores54Position-SpecificScoreMatrix88

ARNDCQEGHILKMFPSTWYV435K-100-1-23030-2-21-1-1-1-1-1-1-1-2436E0102-102-10-1-1000-100-1-1-1437S00-10110110-100020-1-10-1438N-10-1-110-133-1-11-100-1-111-1439K-211-1-20-1-2-2-1-251-2-2-1-1-2-2-1440P-2-2-2-2-3-2-2-2-2-1-2-10-37-1-2-3-1-1441A3-21-20-101-2-2-20-1-2310-3-30442M-3-4-4-4-3-4-4-5-470-410-4-4-2-4-12443A4-4-4-40-4-4-3-44-1-4-2-3-4-1-2-4-34

444H-4-2-1-3-5-2-2-410-6-5-3-4-3-2-3-4-50-5

445R-48-3-40-1-2-3-2-5-40-3-2-4-3-30-4-5

446D-4-4-18-6-20-3-3-5-6-3-5-6-4-2-3-7-5-5

447I-4-5-6-6-3-4-5-6-535-511-5-5-3-4-31

448K001-3-5-1-1-3-3-5-57-4-5-3-1-2-5-4-4

449S0-3-2-30-2-2-3-3-4-4-2-4-5262-5-4-4

450K0301-500-4-1-4-34-3-221-1-5-4-4

451N-4-38-1-5-2-2-3-1-6-6-2-4-5-4-1-2-6-4-5

452I-3-5-5-60-5-5-6-562-52-2-5-4-3-5-33

453M-4-4-6-6-3-4-5-6-506-510-5-4-3-4-30454V-3-3-5-6-3-4-5-6-533-42-2-5-4-3-5-35455K-2114-50-1-21-4-24-3-2-30-1-5-2-3456N1130-4-110-3-4-43-2-5-22-2-5-4-4457D-3-255-1-11-10-5-40-2-5-10-2-6-4-5458L-3-10-30-3-23-4-23011-2-2-35-1-3Position-SpecificScoreMatrixcatalyticloop[>./blastpgp-iNP_499868.2-dnr-j3-QNP_499868.pssm]ARNDCQE89LocalAlignmentStatisticsHighscoresoflocalalignmentsbetweentworandomsequencesfollowtheExtremeValueDistributionScore(S)Alignments(appliestoungappedalignments)E=Kmne-SorE=mn2-S’K=scaleforsearchspace=scaleforscoringsystemS’=bitscore=(S-lnK)/ln2ExpectValueE=numberofdatabasehitsyouexpecttofindbychance,≥SyourscoreexpectednumberofrandomhitsMoreinfo:

/BLAST/tutorial/Altschul-1.html

LocalAlignmentStatisticsHigh90AdvancedBLASTOptions:NucleotideExampleEntrezQueriesnucleotideall[Filter]NOTmammalia[Organism]greenplants[Organism]biomolmrna[Properties]gbdivest[Properties]ANDrat[organism]OtherAdvanced–e10000 expectvalue-v2000 descriptions-b2000 alignmentsAdvancedBLASTOptions:Nucleo91AdvancedBLASTOptions:ProteinMatrixSelectionPAM30--moststringentBLOSUM45--leaststringentExampleEntrezQueriesproteinsall[Filter]NOTmammalia[Organism]greenplants[Organism]srcdbrefseq[Properties]OtherAdvanced–e10000 expectvalue-v2000 descriptions-b2000 alignmentsLimitbytaxonMusmusculus[Organism]Mammalia[Organism]Viridiplantae[Organism]AdvancedBLASTOptions:Protei92sp|P27476|NSR1_YEASTNUCLEARLOCALIZATIONSEQUENCEBINDINGPROTEIN(P67)Length=414Score=40.2bits(92),Expect=0.013Identities=35/131(26%),Positives=56/131(42%),Gaps=4/131(3%)Query:362STTSLTSSSTSGSSDKVYAHQMVRTDSREQKLDAFLQPLSKPLSSQPQAIVTEDKTD418S++SSSS+SSS++++S++SSS++EKSbjct:29SSSSSESSSSSSSSSESESESESESESSSSSSSSDSESSSSSSSDSESEAETKKEESKDS88FilteredUnfilteredLowComplexityFilteringsp|P27476|NSR1_YEASTNUCLEAR93OtherBLASTAlgorithms

MegablastDiscontiguousMegablastPSI-BLASTPHI-BLASTOtherBLASTAlgorithmsMegabla94Megablast:NCBI’sGenomeAnnotator

LongalignmentsofsimilarDNAsequencesGreedyalgorithmConcatenationofquerysequencesFasterthanblastn;lesssensitiveMegablast:NCBI’sGenomeAnnot95MegaBLAST&WordSizeTrade-off:sensitivityvsspeed23blastp828megablast711blastnminimumdefaultWORDSIZEMegaBLAST&WordSizeTrade-off96DiscontiguousMegablastUsesdiscontiguouswordmatchesBetterforcross-speciescomparisonsDiscontiguousMegablastUsesdi97TemplatesforDiscontiguousWordsW=11,t=16,coding: 1101101101101101W=11,t=16,non-coding: 1110010110110111W=12,t=16,coding: 1111101101101101W=12,t=16,non-coding: 1110110110110111W=11,t=18,coding: 101101100101101101W=11,t=18,non-coding: 111010010110010111W=12,t=18,coding: 101101101101101101W=12,t=18,non-coding: 111010110010110111W=11,t=21,coding: 100101100101100101101W=11,t=21,non-coding: 111010010100010010111W=12,t=21,coding: 100101101101100101101W=12,t=21,non-coding: 111010010110010010111Reference:Ma,B,Tromp,J,Li,M.PatternHunter:fasterandmoresensitivehomologysearch.BioinformaticsMarch,2002;18(3):440-5W=wordsize;#matchesintemplatet=templatelengthTemplatesforDiscontiguousWo98Discontiguous(Cross-species)MegaBLASTDiscontiguous(Cross-species)99DiscontiguousWordOptionsDiscontiguousWordOptions100MegaBLASTvsDiscontiguousMegaBLASTNM_017460HomosapienscytochromeP450,family3,subfamilyA,polypeptide4(CYP3A4),transcriptvariant1,mRNA(2768letters)vsDrosophilaMegaBLASTvsDiscontiguousMeg101MegaBLASTvsDiscontiguousMegaBLAST

MegaBLAST=“Nosignificantsimilarityfound.”

DiscontiguousmegaBLAST=MegaBLASTvsDiscontiguousMeg102AnotherExample...

DiscontiguousmegaBLAST=numeroushits...Query:NM_078651DrosophilamelanogasterCG18582-PA(mbt)mRNA,(3244bp)/note=mushroombodiestiny;synonyms:Pak2,STE20,dPAK2

MegaBLAST=“Nosignificantsimilarityfound.”Database:nr(nt),Mammalia[orgn]AnotherExample...Disconti103Ex:DiscontiguousMegaBLASTEx:DiscontiguousMegaBLAST104Ex:BLASTNEx:BLASTN105PSI-BLASTExample:ConfirmingrelationshipsofpurinenucleotidemetabolismproteinsPosition-specificIteratedBLASTPSI-BLASTExample:Confirming106>gi|113340|sp|P03958|ADA_MOUSEADENOSINEDEAMINASE(ADENOSINEMAQTPAFNKPKVELHVHLDGAIKPETILYFGKKRGIALPADTVEELRNIIGMDKPLSLPGFVIAGCREAIKRIAYEFVEMKAKEGVVYVEVRYSPHLLANSKVDPMPWNQTEGDVTPDDVVDEQAFGIKVRSILCCMRHQPSWSLEVLELCKKYNQKTVVAMDLAGDETIEGSSLFPGHVEAYRTVHAGEVGSPEVVREAVDILKTERVGHGYHTIEDEALYNRLLKENMHFEVCPWSSYLTGAVRFKNDKANYSLNTDDPLIFKSTLDTDYQMTKKDMGFTEEEFKRLNINAAKSSFLPEEEKKPSI-BLAST0.005EvaluecutoffforPSSM>gi|113340|sp|P03958|ADA_MOUSE107RESULTS:InitialBLASTPSameresultsasprotein-proteinBLAST;differentformatRESULTS:InitialBLASTPSamere108ResultsofFirstPSSMSearchOtherpurinenucleotidemetabolizingenzymesnotfoundbyordinaryBLASTResultsofFirstPSSMSearchOt109TenthPSSMSearch:ConvergenceJustbelowthreshold,anothernucleotidemetabolismenzymeChecktoaddtoPSSMTenthPSSMSearch:Convergence110ReversePSI-BLAST(RPS)-BLASTReversePSI-BLAST(RPS)-BLAST111Adenosine/AMPDeaminaseDomainAMPDeaminases...Adenosine/AMPDeaminaseDomain112PHI-BLAST>gi|231729|sp|P30429|CED4_CAEELCELLDEATHPROTEIN4MLCEIECRALSTAHTRLIHDFEPRDALTYLEGKNIFTEDHSELISKMSTRLERIANFLRIYRRQASELIDFFNYNNQSHLADFLEDYIDFAINEPDLLRPVVIAPQFSRQMLDRKLLLGNVPKQMTCYIREYHVIKKLDEMCDLDSFFLFLHGRAGSGKSVIASQALSKSDQLIGINYDSIVWLKDSGTAPKSTFDLFTDILKSEDDLLNFPSVEHVTSVVLKRMICNALIDRPNTLFVFDDVVQEETIRWAQELRLRCLVTTRDVEIASQTCEFIEVTSLEIDECYDFLEAYGMPMPVGEKEEDVLNKTIELSSGNPATLMMFFKSCEPKTFEK[GA]xxxxGK[ST]PHI-BLAST>gi|231729|sp|P30429|113What’sNew?What’sNew?114BLASTDatabasesNucleotiderefseq_rna=NM_*,XM_*refseq_genomic=NC_*,NG_*env_ntenvironmental