淀粉樣變性病實(shí)用課件

GenomeResourcesLocusLinkGenedatabaseUniGeneTraceArchiveMapViewerHomologeneGenomeResourcesLocusLinkGene1GenomicBiologyGenomicBiology2淀粉樣變性病實(shí)用課件3淀粉樣變性病實(shí)用課件4淀粉樣變性病實(shí)用課件5GenomeProjects:microbGenomeProjects:microb6淀粉樣變性病實(shí)用課件7=scaleforscoringsystemNegativeforlesslikelysubstitutionsOtherpurinenucleotidemetabolizingenzymesnotfoundbyordinaryBLASTMusmusculus[Organism]G0-20-1-3-2-26nucleotide,proteinandtranslations(blastn,blastp,blastx,tblastn,tblastx)environmentalsample[filter],e.GTACTGGACATSbjct287LEETYAKYLHKGASYFVYLSLNMSPEQLDVNVHPSKRIVHFLYDQEI333catalyticloopG0-20-1-3-2-26Wordsize=3(default)refseq_genomic=NC_*,NG_*EntrezGeneEntrezlinksDrosophilamelanogasterCG18582-PA(mbt)mRNA,(3244bp)WhyDoWeNeed

SequenceSimilaritySearching?UniGeneClusterHs.ServiceAddresses95351:seqs=scaleforscoringsystem8GenomeResourcesLocusLinkGenedatabaseUniGeneTraceArchiveMapViewerHomologeneGenomeResourcesLocusLinkGene9451N-4-38-1-5-2-2-3-1-6-6-2-4-5-4-1-2-6-4-5Nucleotideonly:-e10000-v2000ATCACCATGAAGTGGCTGAAGGATAAGCAGCCAATGGATGCCAAGGAGTTCGAACCTAAAGACGTATTGCCCAATGGGGATGGGACBasicLocalAlignmentSearchToolbiomolmrna[Properties]Sbjct287LEETYAKYLHKGASYFVYLSLNMSPEQLDVNVHPSKRIVHFLYDQEI333RESULTS:InitialBLASTPSpecies NumberofgenesW=11,t=18,non-coding: 111010010110010111Makelookuptableof“words”forquerySsc_UniGenevsDrosophilaWhitehead-RHGTQITVEDLFYNIATRRKALKNSerine/ThreonineproteinkinasesGTACTGGACATGGACCCTACAGGAALKSEDDLLNFPSVEHVTSVVLKRMICNALIDRPNTLFVFDDVVQEETIRWAQELRLRCLVTTRDVEIAsinglequeryinterfaceto…

Sequences -RefSeqs -GenBank -HomologeneMaps–MapViewerEntrezlinksLocusLinkLocusLinkwillbereplacedbyEntrezGeneonMARCH1,2005.CheckGeneFAQforcurrentinformation.451N-4-38-1-5-2-2-10EntrezGeneLocusLinkAsinglequeryinterfaceto…

Sequences-RefSeqs-GenBank-HomologeneMaps–MapViewer EntrezlinksEntrezGene

Moreorganisms-allRefSeqgenomesEntrezintegrationEntrezGeneLocusLinkAsingleq11Gsn[sym]淀粉樣變性病Gsn[sym]淀粉樣變性病12淀粉樣變性病實(shí)用課件13GlobalEntrez:NADH2nadh247GlobalEntrez:NADH2nadh24714EntrezGene:NADH226recordsEntrezGene:NADH226records15GeneRecordforPongoNADH2HomosapiensGeneRecordforPongoNADH2Hom16DisplayExons/Introns:GeneTableDisplayExons/Introns:GeneT17GeneTableGeneTable18ARecordWithMoreData:HumanHFE血色沉著病ARecordWithMoreData:Human19GeneGraphicLinksNM_NP_GeneGraphicLinksNM_NP_20Introns/Exons:GeneTablelinkstosequenceIntrons/Exons:GeneTablelin21Gga_UniGeneFindsbestlocalalignmentsGTACTGGACAT441A3-21-20-101-2-2-20-1-2310-3-30H-201-1-300-28TheNewHomologeneJustbelowthreshold,anotherSsc_UniGenesp|P27476|NSR1_YEASTNUCLEARLOCALIZATIONSEQUENCEBINDINGPROTEIN(P67)OtherBLASTAlgorithmsYLSHFLIdentitymatrix450K0301-500-4-1-4-34-3-221-1-5-4-4TraceArchiveStrongylocentrotuspurpuratusTracesMegaBLAST=“Nosignificantsimilarityfound.Nucleotideonly:grayline=samedatabasehitProvidesstatisticalsignificancecatalyticloopBasicLocalAlignmentSearchToolARecordWithMoreData:HumanHFEGga_UniGeneARecordWithMore22EntrezSNPhfe[genename]ANDhuman[orgn]52血色沉著病EntrezSNPhfe[genename]ANDh23LinkingtoSNP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24SNPinStructureSNPinStructure25LinktoOMIMLinktoOMIM26VariantsinOMIMVariantsinOMIM27GenomeResourcesLocusLinkGenedatabaseTraceArchiveMapViewerHomologeneUniGeneGenomeResourcesLocusLinkGene28ACATGGACCCTGTQITVEDLFYNI=scaleforscoringsystem>gi|113340|sp|P03958|ADA_MOUSEADENOSINEDEAMINASE(ADENOSINE435K-100-1-23030-2-21-1-1-1-1-1-1-1-2TheNewHomologeneBLOSUM62-defaultmatrixforBLASTTrade-off:sensitivityvsspeedSsc_UniGeneRAG1→HomologeneDiscontiguous(Cross-species)MegaBLASTDisplayExons/Introns:GeneTableMammalia[Organism]biomolmrna[Properties]UniGeneClusterHs.sp|P27476|NSR1_YEASTNUCLEARLOCALIZATIONSEQUENCEBINDINGPROTEIN(P67)GTQITVEDLFYNILimitbytaxonEntrezGene:NADH2Musmusculus[Organism]Gene-orientedclustersofexpressedsequences

AutomaticclusteringusingMegaBlastEachclusterrepresentsauniquegeneInformedbygenomehitsInformationontissuetypesandmaplocationsUsefulforgenediscoveryandselectionofmapping reagentsUniGeneACATGGACCCTGene-orientedclust29Seq1: 1W--HEREISWALTERNOW16NolongerUniGenebasedoptimizedforlargebatchsearchesL-1-2-3-4-1-2-3-4-324[GA]xxxxGK[ST]nucleotidemetabolismproteinsChecktoaddtoPSSMcatalyticloopcheckprimerspecificityinsilicoIdentitymatrixWordsizecanonlybe2or3[-f11=blastpdefault]W=12,t=21,coding: 100101101101100101101BLOSUM62-defaultmatrixforBLASTGlobalvsLocalAlignment452I-3-5-5-60-5-5-6-562-52-2-5-4-3-5-33GTQITVEDLFYNIDerivedfromobservation;smalldatasetof alignmentsStandardBLASTG0-20-1-3-2-26AClusterofESTsquery5’ESThits3’ESThitsSeq1: 1W--HERE30UnigeneUnigene31UniGeneCollectionsUniGeneCollections32ExampleUniGeneClusterExampleUniGeneCluster33HistogramofclustersizesforUniGeneHsbuild177Histogramofclustersizesfor34X0-1-1-1-2-1-1-1-1-1-1-1-1-1-200-2-1-1-1458L-3-10-30-3-23-4-23011-2-2-35-1-3DiscontiguousMegablastLTV,MTV,ISV,LSV,etc.ARNDCQEGHILKMFPSTWYVJustbelowthreshold,anotherHumanGenomeBLAST:ResultsverysensitiveproteinsearchDiscontiguousmegaBLAST=GenedatabaseGeneralHelpProteinvsDNAtranslationtblastn446D-4-4-18-6-20-3-3-5-6-3-5-6-4-2-3-7-5-5H-201-1-300-28441A3-21-20-101-2-2-20-1-2310-3-30=scaleforscoringsystemHomolgene:RAG1W=wordsize;#matchesintemplateGTQITVEDLFYNISequenceView(sv)UniGeneClusterHs.95351X0-1-1-1-2-1-1-1-1-35UniGeneClusterHs.95351UniGeneClusterHs.9535136UniGeneClusterHs.95351:expressionUniGeneClusterHs.95351:expr37UniGeneClusterHs.95351:seqsUniGeneClusterHs.95351:seqs38DownloadsequenceswebpageftpsiteDownloadsequenceswebpageftp39GenomeResourcesLocusLinkGenedatabaseUniGeneTraceArchiveMapViewerHomologeneGenomeResourcesLocusLinkGene40TheNewHomologeneAutomateddetectionofhomologsamongtheannotatedgenesofcompletelysequencedeukaryoticgenomes.NolongerUniGenebasedProteinsimilaritiesfirstGuidedbytaxonomictreeIncludesorthologsandparalogsTheNewHomologeneAutomatedde41

Orthologs和Paralogs是同源序列的兩種類型。

Orthologs（垂直同源基因）是指來(lái)自于不同物種的由垂直家系（物種形成）進(jìn)化而來(lái)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(lái)源于基因復(fù)制的蛋白，可能會(huì)進(jìn)化出新的與原來(lái)有關(guān)的功能。請(qǐng)參考文獻(xiàn)獲得更多的信息。Orthologs和Paralogs42geneduplicationParalogsvsOrthologsearlyglobingeneA-chaingene B-chaingenefrogAchickAmouseAmouse

BchickBfrogBparalogsorthologs

orthologsgeneduplicationParalogsvsOr43TheNewHomologeneHomologeneBuild37.2Species Numberofgenes inputgrouped groupsTheNewHomologene44GlobalvsLocalAlignmentHumanGenomeBLAST:ResultsreverseprimerBasicLocalAlignmentSearchToolSeq1: 1W--HEREISWALTERNOW16GTQITVEDLFYNIreverseprimerAllcombinations(DNA/Protein)queryanddatabase.“hemochromatosis”Sbjct287LEETYAKYLHKGASYFVYLSLNMSPEQLDVNVHPSKRIVHFLYDQEI333--GeneticMaps--W=wordsize;#matchesintemplateStandardBLASTMegaBLASTvsDiscontiguousMegaBLASTProteinBLASTrequirestwoneighboringmatcheswithin40aaX0-1-1-1-2-1-1-1-1-1-1-1-1-1-200-2-1-1-1-b2000 alignmentsARecordWithMoreData:HumanHFEWayneMatten456N1130-4-110-3-4-43-2-5-22-2-5-4-4RAG1→Homologenerag112recombinationactivatinggeneGlobalvsLocalAlignmentRAG145RAG1→HomolgeneRAG1AmniotaRAG1→HomolgeneRAG1Amniota46Homolgene:RAG1Homolgene:RAG147淀粉樣變性病實(shí)用課件48Homolgene:RAG1Homolgene:RAG149GenomeResourcesLocusLinkGenedatabaseUniGeneTraceArchiveMapViewerHomologeneGenomeResourcesLocusLinkGene50淀粉樣變性病實(shí)用課件51淀粉樣變性病實(shí)用課件52淀粉樣變性病實(shí)用課件53MapViewerMapViewer54ListViewListView55Moreinfo:Ex:BLASTNMammalia[Organism]GenomeResourcesMegaBLAST=“Nosignificantsimilarityfound.GenomeResourcesStandford-G3441A3-21-20-101-2-2-20-1-2310-3-30||||||||||||||||||| rawscore=19-9=10GenomeResourcesProvidesstatisticalsignificanceDisplayExons/Introns:GeneTableMusmusculus[Organism]K=scaleforsearchspacegov/gene/DATA/gene_info.Species NumberofgenesUniGeneClusterHs.A+1–3–3-3HumanMapVieweradar腺甙脫氨酶Moreinfo:HumanMapVieweradar腺56MapViewer:HumanADAR4MapViewer:HumanADAR457MVHsADAR3’UTR5’UTRMVHsADAR3’UTR5’UTR58Maps&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-59MapViewerUniGeneComponentRepeatsGeneMapViewerUniGeneComponentRepea60Mastermap:repeatsMastermap:repeats61GenePhenotypeVariationGenePhenotypeVariation62W=12,t=18,coding: 101101101101101101[GA]xxxxGK[ST]CAGGTAGCAAGCTTGCATGTCATraceArchiverecombinationactivatinggeneUniGeneClusterHs.446D-4-4-18-6-20-3-3-5-6-3-5-6-4-2-3-7-5-5DNAtranslationvsDNAtranslationtblastxK=scaleforsearchspaceGenomicBiology2bits(92),Expect=0.Sbjct287LEETYAKYLHKGASYFVYLSLNMSPEQLDVNVHPSKRIVHFLYDQEI333refseq_genomic=NC_*,NG_*441A3-21-20-101-2-2-20-1-2310-3-30BLASTstatisticsrayfinnedfishes[Organism]Particularlyusefulfornucleotidesequenceswithout440P-2-2-2-2-3-2-2-2-2-1-2-10-37-1-2-3-1-1CATGCTTAATTAllcombinations(DNA/Protein)queryanddatabase.PAM250widelyusedMaps&OptionsMaps&OptionsW=12,t=18,coding: 1011063GenomeResourcesLocusLinkGenedatabaseUniGeneTraceArchiveMapViewerHomologeneGenomeResourcesLocusLinkGene64淀粉樣變性病實(shí)用課件65淀粉樣變性病實(shí)用課件66Strongylocentrotuspurpuratus

TracesStrongylocentrotuspurpuratus67BLASTBasicLocalAlignmentSearchToolBLASTBasicLocalAlignmentSea68WebAccessBLASTVASTEntrezTextSequenceStructureWebAccessBLASTVASTEntrezTextS69淀粉樣變性病實(shí)用課件70BasicLocalAlignmentSearchToolWhyusesequencesimilarity?BLASTalgorithmBLASTstatisticsBLASToutputExamplesBasicLocalAlignmentSearchT71WhyDoWeNeed

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

SequenceSimil72BLASTWebsiteStatsBLASTWebsiteStats73GlobalvsLocalAlignmentSeq1Seq2Seq1Seq2GlobalalignmentLocalalignmentGlobalvsLocalAlignmentSeq174GlobalvsLocalAlignmentSeq1:WHEREISWALTERNOW(16aa)Seq2:HEWASHEREBUTNOWISHERE(21aa)GlobalSeq1: 1W--HEREISWALTERNOW16 WHERESeq2: 1HEWASHEREBUTNOWISHERE21LocalSeq1:1W--HERE5Seq1:1W--HERE5WHEREWHERESeq2:3WASHERE9Seq2:15WISHERE21GlobalvsLocalAlignmentSeq1:75TheFlavorsofBLASTStandardBLASTtraditional“contiguous”wordhitpositionindependentscoringnucleotide,proteinandtranslations(blastn,blastp,blastx,tblastn,tblastx)MegablastoptimizedforlargebatchsearchescanusediscontiguouswordsPSI-BLASTconstructsPSSMsautomatically;usesasqueryverysensitiveproteinsearchRPSBLASTsearchesadatabaseofPSSMstoolforconserveddomainsearchesTheFlavorsofBLASTStandardB76WidelyusedsimilaritysearchtoolHeuristicapproachbasedonSmithWatermanalgorithmFindsbestlocalalignmentsProvidesstatisticalsignificanceAllcombinations(DNA/Protein)queryanddatabase.DNAvsDNA

blastnDNAtranslationvsProteinblastxProteinvsProteinblastpProteinvsDNAtranslationtblastnDNAtranslationvsDNAtranslationtblastx

www,standalone,andnetworkclientsBasicLocalAlignmentSearchToolWidelyusedsimilaritysearch77TranslatedBLASTQueryDatabaseProgramNPucleotideroteinNNNNPPblastxtblastntblastxPPPPPPPPPPPPPPPPPPPPPPPPParticularlyusefulfornucleotidesequenceswithoutproteinannotations,suchasESTsorgenomicDNATranslatedBLASTQueryDatabaseP78HowBLASTWorksMakelookuptableof“words”forqueryScandatabaseforhitsUngappedextensionsofhits(initialHSPs)Gappedextensions(notraceback)Gappedextensions(traceback;alignmentdetails)HowBLASTWorksMakelookuptab79NucleotideWordsGTACTGGACATGGACCCTACAGGAAQuery:GTACTGGACATTACTGGACATGACTGGACATGGCTGGACATGGATGGACATGGACGGACATGGACCGACATGGACCCACATGGACCCTMakealookuptableofwords11-mer...828megablast711blastnminimumdefaultWORDSIZENucleotideWordsGTACTGGACATGGA80ProteinWordsGTQITVEDLFYNIATRRKALKNQuery:

NeighborhoodWordsLTV,MTV,ISV,LSV,etc.GTQTQIQITITVTVEVEDEDLDLF...MakealookuptableofwordsWordsize=3(default)Wordsizecanonlybe2or3[-f11=blastpdefault]ProteinWordsGTQITVEDLFYNIATRR81MinimumRequirementsforaHitNucleotideBLASTrequiresoneexactmatchProteinBLASTrequirestwoneighboringmatcheswithin40aaGTQITVEDLFYNI

SEIYYNATCGCCATGCTTAATTGGGCTT

CATGCTTAATT

neighborhoodwordsoneexactmatchtwomatches[-A40=blastpdefault]MinimumRequirementsforaHit82BLASTPSummary

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…examplequerywordsBLASTPSummary83ScoringSystems-NucleotidesAGCTA+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-Nucleotides84ScoringSystems-ProteinsPositionIndependentMatricesPAMMatrices(PercentAcceptedMutation)Derivedfromobservation;smalldatasetof alignmentsImplicitmodelofevolutionAllcalculatedfromPAM1PAM250widelyusedBLOSUMMatrices(BLOckSUbstitutionMatrices)Derivedfromobservation;largedatasetofhighly conservedblocksEachmatrixderivedseparatelyfromblockswitha definedpercentidentitycutoffBLOSUM62-defaultmatrixforBLASTPositionSpecificScoreMatrices(PSSMs)

PSI-andRPS-BLASTScoringSystems-ProteinsPosi85A4R-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-2-2-2-3-2-1-2-32-1-1-2-13-3-2-227V0-3-3-3-1-2-2-3-331-21-1-2-20-3-14X0-1-1-1-2-1-1-1-1-1-1-1-1-1-200-2-1-1-1ARNDCQEGHILKMFPSTWYVXBLOSUM62DFNegativeforlesslikelysubstitutionsDYFPositiveformorelikelysubstitutionsA4BLOSUM62DFNegativeforles86Position-SpecificScoreMatrixDAF-1Serine/Threonineproteinkinasescatalyticloop174PSSMscores54Position-SpecificScoreMatrix87ARNDCQEGHILKMFPSTWYV435K-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]ARNDCQE88LocalAlignmentStatisticsHighscoresoflocalalignmentsbetweentworandomsequencesfollowtheExtremeValueDistributionScore(S)Alignments(appliestoungappedalignments)E=Kmne-SorE=mn2-S’K=scaleforsearchspace=scaleforscoringsystemS’=bitscore=(S-lnK)/ln2ExpectValueE=numberofdatabasehitsyouexpecttofindbychance,≥SyourscoreexpectednumberofrandomhitsMoreinfo:

LocalAlignmentStatisticsHigh89AdvancedBLASTOptions:NucleotideExampleEntrezQueriesnucleotideall[Filter]NOTmammalia[Organism]greenplants[Organism]biomolmrna[Properties]gbdivest[Properties]ANDrat[organism]OtherAdvanced–e10000 expectvalue-v2000 descriptions-b2000 alignmentsAdvancedBLASTOptions:Nucleo90AdvancedBLASTOptions:ProteinMatrixSelectionPAM30--moststringentBLOSUM45--leaststringentExampleEntrezQueriesproteinsall[Filter]NOTmammalia[Organism]greenplants[Organism]srcdbrefseq[Properties]OtherAdvanced–e10000 expectvalue-v2000 descriptions-b2000 alignmentsLimitbytaxonMusmusculus[Organism]Mammalia[Organism]Viridiplantae[Organism]AdvancedBLASTOptions:Protei91sp|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_YEASTNUCLEAR92OtherBLASTAlgorithms

MegablastDiscontiguousMegablastPSI-BLASTPHI-BLASTOtherBLASTAlgorithmsMegabla93Megablast:NCBI’sGenomeAnnotator

LongalignmentsofsimilarDNAsequencesGreedyalgorithmConcatenationofquerysequencesFasterthanblastn;lesssensitiveMegablast:NCBI’sGenomeAnnot94MegaBLAST&WordSizeTrade-off:sensitivityvsspeed23blastp828megablast711blastnminimumdefaultWORDSIZEMegaBLAST&WordSizeTrade-off95DiscontiguousMegablastUsesdiscontiguouswordmatchesBetterforcross-speciescomparisonsDiscontiguousMegablastUsesdi96TemplatesforDiscontiguousWordsW=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=templatelengthTemplatesforDiscontiguousWo97Discontiguous(Cross-species)MegaBLASTDiscontiguous(Cross-species)98DiscontiguousWordOptionsDiscontiguousWordOptions99MegaBLASTvsDiscontiguousMegaBLASTNM_017460HomosapienscytochromeP450,family3,subfamilyA,polypeptide4(CYP3A4),transcriptvariant1,mRNA(2768letters)vsDrosophilaMegaBLASTvsDiscontiguousMeg100MegaBLASTvsDiscontiguousMegaBLASTMegaBLAST=“Nosignificantsimilarityfound.”DiscontiguousmegaBLAST=MegaBLASTvsDiscontiguousMeg101AnotherExample...DiscontiguousmegaBLAST=numeroushits...Query:NM_078651DrosophilamelanogasterCG18582-PA(mbt)mRNA,(3244bp)/note=mushroombodiestiny;synonyms:Pak2,STE20,dPAK2MegaBLAST=“Nosignificantsimilarityfound.”Database:nr(nt),Mammalia[orgn]AnotherExample...Disconti102Ex:DiscontiguousMegaBLASTEx:DiscontiguousMegaBLAST103Ex:BLASTNEx:BLASTN104PSI-BLASTExample:ConfirmingrelationshipsofpurinenucleotidemetabolismproteinsPosition-specificIteratedBLASTPSI-BLASTExample:Confirming105>gi|113340|sp|P03958|ADA_MOUSEADENOSINEDEAMINASE(ADENOSINEMAQTPAFNKPKVELHVHLDGAIKPETILYFGKKRGIALPADTVEELRNIIGMDKPLSLPGFVIAGCREAIKRIAYEFVEMKAKEGVVYVEVRYSPHLLANSKVDPMPWNQTEGDVTPDDVVDEQAFGIKVRSILCCMRHQPSWSLEVLELCKKYNQKTVVAMDLAGDETIEGSSLFPGHVEAYRTVHAGEVGSPEVVREAVDILKTERVGHGYHTIEDEALYNRLLKENMHFEVCPWSSYLTGAVRFKNDKANYSLNTDDPLIFKSTLDTDYQMTKKDMGFTEEEFKRLNINAAKSSFLPEEEKKPSI-BLAST0.005EvaluecutoffforPSSM>gi|113340|sp|P03958|ADA_MOUSE106RESULTS:InitialBLASTPSameresultsasprotein-proteinBLAST;differentformatRESULTS:InitialBLASTPSamere107ResultsofFirstPSSMSearchOtherpurinenucleotidemetabolizingenzymesnotfoundbyordinaryBLASTResultsofFirstPSSMSearchOt108TenthPSSMSearch:ConvergenceJustbelowthreshold,anothernucleotidemetabolismenzymeChecktoaddtoPSSMTenthPSSMSearch:Convergence109ReversePSI-BLAST(RPS)-BLASTReversePSI-BLAST(RPS)-BLAST110Adenosine/AMPDeaminaseDomainAMPDeaminases...Adenosine/AMPDeaminaseDomain111PHI-BLAST>gi|231729|sp|P30429|CED4_CAEELCELLDEATHPROTEIN4MLCEIECRALSTAHTRLIHDFEPRDALTYLEGKNIFTEDHSELISKMSTRLERIANFLRIYRRQASELIDFFNYNNQSHLADFLEDYIDFAINEPDLLRPVVIAPQFSRQMLDRKLLLGNVPKQMTCYIREYHVIKKLDEMCDLDSFFLFLHGRAGSGKSVIASQALSKSDQLIGINYDSIVWLKDSGTAPKSTFDLFTDILKSEDDLLNFPSVEHVTSVVLKRMICNALIDRPNTLFVFDDVVQEETIRWAQELRLRCLVTTRDVEIASQTCEFIEVTSLEIDECYDFLEAYGMPMPVGEKEEDVLNKTIELSSGNPATLMMFFKSCEPKTFEK[GA]xxxxGK[ST]PHI-BLAST>gi|231729|sp|P30429|112What’sNew?What’sNew?113BLASTDatabasesNucleotiderefseq_rna=NM_*,XM_*refseq_genomic=NC_*,NG_*env_ntenvironmentalsample[filter],e.g.,16SrRNAProteinrefseq=NP_*,XP_*env_nrBLASTDatabasesNucleotide114NewFormatterSelectlowercaseSelectredNewFormatterSelectlowercase115NewFormattergrayline=samedatabasehithsp’scolor-codedindependentlyNewFormattergrayline=same116BLASTOutput:Alignments&FilterlowcomplexitysequencefilteredBLASTOutput:Alignments&Fil117AdvancedOptionsLimittoOrganismproteinall[filter]NExampleEntrezQueries

proteinsall[Filter]NOTmammalia[Organism] rayfinnedfishes[Organism] srcdbrefseq[Properties]Nucleotideonly:

biomolmrna[Properties]

biomolgenomic[Properties]OtherAdvanced –e10000 expectvalue -v2000 descriptions -b2000 alignments-e10000-v2000AdvancedOptionsLimittoOrgan118GenomeBLASTExamplesGenomeBLASTExamples119ExampleSearchPathways:HemochromatosisGeneOMIMGene“hemochromatosis”nucleotidesequenceGenomeBLASTMapViewerSNPProteinDomainstextsearchsequencesearchExampleSearchPathways:Hemoc120SampleSample121Example:HumanGenomeBLAST

TGCCTCCTTTGGTGAAGGTGACACATCATGTGACCTCTTCAGTGACCACTCTACGGTGTCGGGCCTTGAACTACTACCCCCAGAACATCACCATGAAGTGGCTGAAGGATAAGCAGCCAATGGATGCCAAGGAGTTCGAACCTAAAGACGTATTGCCCAATGGGGATGGGACCTACCAGGGCTGGATAACCTTGGCTGTACCCCCTGGGGAAGAGCHumanESTExample:HumanGenomeBLASTTG122HumanGenomeBLAST:Results

HumanGenomeBLAST:Results123HumanGenomeBLAST:MapViewerEntrezGeneHumanGenomeBLAST:MapViewerE124MapOligosOntoGenome>CCATGGCGACCCTGG