《淀粉样变性病》PPT课件.ppt

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1、NCBI FieldGuideA Field Guide Genome resources Sequence similarityNCBI FieldGuideGenome ResourcesLocusLinkLocusLinkLocusLinkLocusLinkGene databaseGene databaseGene databaseGene databaseUniGeneUniGeneUniGeneUniGeneTrace ArchiveTrace ArchiveTrace ArchiveTrace ArchiveMap ViewerMap ViewerMap ViewerMap Vi

2、ewerHomologeneHomologeneHomologeneHomologeneNCBI FieldGuideGenomic BiologyNCBI FieldGuideNCBI FieldGuideNCBI FieldGuideNCBI FieldGuideGenome Projects:microbNCBI FieldGuideNCBI FieldGuideNCBI FieldGuideGenome ResourcesLocusLinkLocusLinkLocusLinkLocusLinkGene databaseGene databaseGene databaseGene dat

3、abaseUniGeneUniGeneUniGeneUniGeneTrace ArchiveTrace ArchiveTrace ArchiveTrace ArchiveMap ViewerMap ViewerMap ViewerMap ViewerHomologeneHomologeneHomologeneHomologeneNCBI FieldGuideA single query interface to SequencesSequences-RefSeqs-RefSeqs-GenBank-GenBank-HomologeneHomologeneMaps Maps MapViewerMa

4、pViewerEntrez linksEntrez linksLocusLinkLocusLink will be replaced by Entrez Gene on MARCH 1,2005.Check Gene FAQ for current information.NCBI FieldGuideEntrez GeneLocusLinkA single query interface to SequencesSequences -RefSeqs -RefSeqs -GenBank -GenBank -HomologeneHomologeneMaps Maps MapViewerMapVi

5、ewerEntrez linksEntrez linksEntrez Gene More organisms-all RefSeq genomes Entrez integrationNCBI FieldGuideGsnsym淀粉样变性病NCBI FieldGuideNCBI FieldGuideGlobal Entrez:NADH2nadh247NCBI FieldGuideEntrez Gene:NADH226 recordsNCBI FieldGuideGene Record for Pongo NADH2Homo sapiensNCBI FieldGuideDisplay Exons/

6、Introns:Gene TableNCBI FieldGuideGene TableNCBI FieldGuideA Record With More Data:Human HFE血色沉着病NCBI FieldGuideGene Graphic LinksNM_NM_NP_NP_NCBI FieldGuideIntrons/Exons:Gene Tablelinks to sequenceNCBI FieldGuideA Record With More Data:Human HFENCBI FieldGuideEntrez SNPhfegene name AND humanorgn 52血

7、色沉着病NCBI FieldGuideLinking to SNP染色体定位基因定位序列定位NCBI FieldGuideSNP in StructureNCBI FieldGuideLink to OMIMNCBI FieldGuideVariants in OMIMNCBI FieldGuideGenome ResourcesLocusLinkLocusLinkLocusLinkLocusLinkGene databaseGene databaseGene databaseGene databaseTrace ArchiveTrace ArchiveTrace ArchiveTrace A

8、rchiveMap ViewerMap ViewerMap ViewerMap ViewerHomologeneHomologeneHomologeneHomologeneUniGeneUniGeneNCBI FieldGuideGene-oriented clusters of expressed sequences Automatic clustering using MegaBlast Each cluster represents a unique gene Informed by genome hits Information on tissue types and map loca

9、tions Useful for gene discovery and selection of mapping reagentsUniGeneNCBI FieldGuideA Cluster of ESTsquery5 EST hits3 EST hitsNCBI FieldGuideUnigeneNCBI FieldGuideUniGene CollectionsNCBI FieldGuideExample UniGene ClusterNCBI FieldGuideHistogram of cluster sizes for UniGene Hs build 177NCBI FieldG

10、uideUniGene Cluster Hs.95351NCBI FieldGuideUniGene Cluster Hs.95351NCBI FieldGuideUniGene Cluster Hs.95351:expressionNCBI FieldGuideUniGene Cluster Hs.95351:seqsNCBI FieldGuideDownload sequencesweb pageftp siteNCBI FieldGuideGenome ResourcesLocusLinkLocusLinkLocusLinkLocusLinkGene databaseGene datab

11、aseGene databaseGene databaseUniGeneUniGeneUniGeneUniGeneTrace ArchiveTrace ArchiveTrace ArchiveTrace ArchiveMap ViewerMap ViewerMap ViewerMap ViewerHomologeneHomologeneHomologeneHomologeneNCBI FieldGuideThe New HomologeneAutomated detection of homologs among the annotated genes of completely sequen

12、ced eukaryotic genomes.No longer UniGene basedProtein similarities firstGuided by taxonomic treeIncludes orthologs and paralogsNCBI FieldGuide 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

13、得更多的信息。NCBI FieldGuidegene duplicationParalogs vs Orthologsearly globin geneA-chain gene B-chain genefrog A chick A mouse Amouse B chick B frog Bparalogsorthologs orthologsNCBI FieldGuideThe New Homologene Homologene Build 37.2Species Number of genes input grouped groupsNCBI FieldGuideRAG1 Homologen

14、erag112recombination activating gene NCBI FieldGuideRAG1 HomolgeneRAG1Amniota NCBI FieldGuideHomolgene:RAG1NCBI FieldGuideNCBI FieldGuideHomolgene:RAG1NCBI FieldGuideGenome ResourcesLocusLinkLocusLinkLocusLinkLocusLinkGene databaseGene databaseGene databaseGene databaseUniGeneUniGeneUniGeneUniGeneTr

15、ace ArchiveTrace ArchiveTrace ArchiveTrace ArchiveMap ViewerMap ViewerMap ViewerMap ViewerHomologeneHomologeneHomologeneHomologeneNCBI FieldGuideNCBI FieldGuideNCBI FieldGuideNCBI FieldGuideMapViewerNCBI FieldGuideList ViewNCBI FieldGuideHuman MapVieweradar腺甙脱氨酶NCBI FieldGuideMapViewer:Human ADAR4NC

16、BI FieldGuideMV Hs ADAR3 UTR5 UTRNCBI FieldGuideMaps&Options-Sequence mapsSequence maps-Ab initioAssemblyRepeatsBES_CloneCloneNCI_CloneContigComponentCpG islanddbSNP haplotypeFosmidGenBank_DNAGenePhenotypeSAGE_TagSTSTCAG_RNATranscript(RNA)Hs_UniGeneHs_EST-Cytogenetic mapsCytogenetic maps-IdeogramFIS

17、H CloneGene_CytogeneticMitelman BreakpointMorbid/Disease-Genetic Maps-deCODEGenethonMarshfield-RH maps-GeneMap99-G3GeneMap99-GB4NCBI RHStandford-G3TNGWhitehead-RHWhitehead-YACMm_UniGeneMm_ESTRn_UniGeneRn_ESTSsc_UniGeneSsc_ESTBt_UniGeneBt_ESTGga_UniGeneGga_ESTVariationMaps&Options=SNPNCBI FieldGuideM

18、apViewerUniGeneComponentRepeatsGeneNCBI FieldGuideMaster map:repeatsNCBI FieldGuideGenePhenotypeVariationNCBI FieldGuideMaps&OptionsMaps&OptionsNCBI FieldGuideGenome ResourcesLocusLinkLocusLinkLocusLinkLocusLinkGene databaseGene databaseGene databaseGene databaseUniGeneUniGeneUniGeneUniGeneTrace Arc

19、hiveTrace ArchiveTrace ArchiveTrace ArchiveMap ViewerMap ViewerMap ViewerMap ViewerHomologeneHomologeneHomologeneHomologeneNCBI FieldGuideNCBI FieldGuideNCBI FieldGuideStrongylocentrotus purpuratus TracesNCBI FieldGuideBLASTBasic Local Alignment Search ToolNCBI FieldGuideWeb AccessBLASTVASTEntrezTex

20、tSequenceStructureNCBI FieldGuideNCBI FieldGuideBasic Local Alignment Search Tool Why use sequence similarity?BLAST algorithm BLAST statistics BLAST output ExamplesNCBI FieldGuideWhy Do We Need Sequence Similarity Searching?To identify and annotate sequencesTo evaluate evolutionary relationshipsOthe

21、r:model genomic structure(e.g.,Spidey)check primer specificity in silico:NCBIs toolNCBI FieldGuideBLAST Website StatsNCBI FieldGuideGlobal vs Local AlignmentSeq 1Seq 2Seq 1Seq 2Global alignmentLocal alignmentNCBI FieldGuideGlobal vs Local AlignmentSeq1:WHEREISWALTERNOW (16aa)Seq2:HEWASHEREBUTNOWISHE

22、RE(21aa)GlobalSeq1:1 W-HEREISWALTERNOW 16 W HERE Seq2:1 HEWASHEREBUTNOWISHERE 21LocalSeq1:1 W-HERE 5 Seq1:1 W-HERE 5 W HERE W HERESeq2:3 WASHERE 9 Seq2:15 WISHERE 21NCBI FieldGuideThe Flavors of BLASTStandard BLASTtraditional“contiguous”word hitposition independent scoring nucleotide,protein and tra

23、nslations(blastn,blastp,blastx,tblastn,tblastx)Megablastoptimized for large batch searchescan use discontiguous wordsPSI-BLASTconstructs PSSMs automatically;uses as queryvery sensitive protein searchRPS BLASTsearches a database of PSSMstool for conserved domain searchesNCBI FieldGuideWidely used sim

24、ilarity search toolHeuristic approach based on Smith Waterman algorithmFinds best local alignmentsProvides statistical significanceAll combinations(DNA/Protein)query and database.DNA vs DNA blastnDNA translation vs Protein blastxProtein vs Protein blastpProtein vs DNA translation tblastnDNA translat

25、ion vs DNA translation tblastx www,standalone,and network clientsBasic Local Alignment Search ToolNCBI FieldGuideTranslated BLASTQueryQueryDatabaseDatabaseProgramProgramNPucleotideroteinNNNNPPblastxtblastntblastxPPPPPPPPPPPPPPPPPPPPPPPPParticularly useful for nucleotide sequences withoutprotein anno

26、tations,such as ESTs or genomic DNANCBI FieldGuideHow BLAST WorksMake lookup table of“words”for queryScan database for hitsUngapped extensions of hits(initial HSPs)Gapped extensions(no traceback)Gapped extensions(traceback;alignment details)NCBI FieldGuideNucleotide WordsGTACTGGACATGGACCCTACAGGAAQue

27、ry:GTACTGGACAT TACTGGACATG ACTGGACATGG CTGGACATGGA TGGACATGGAC GGACATGGACC GACATGGACCC ACATGGACCCTMake a lookuptable of words11-mer.828megablast711blastnminimumdefaultWORD SIZENCBI FieldGuideProtein WordsGTQITVEDLFYNIATRRKALKNQuery:Neighborhood WordsLTV,MTV,ISV,LSV,etc.GTQ TQI QIT ITV TVE VED EDL DL

28、F .Make a lookuptable of wordsWord size=3(default)Word size can only be 2 or 3-f 11=blastp default NCBI FieldGuideMinimum Requirements for a Hit Nucleotide BLAST requires one exact match Protein BLAST requires two neighboring matches within 40 aaGTQITVEDLFYNI SEI YYNATCGCCATGCTTAATTGGGCTT CATGCTTAAT

29、T neighborhood wordsone exact matchtwo matches-A 40=blastp default NCBI FieldGuideBLASTP Summary YLS HFLSbjct 287 LEETYAKYLHKGASYFVYLSLNMSPEQLDVNVHPSKRIVHFLYDQEI 333 Query 1 IETVYAAYLPKNTHPFLYLSLEISPQNVDVNVHPTKHEVHFLHEESI 47Gapped extension with trace backGapped extension with trace backQuery 1 IETV

30、YAAYLPKNTHPFLYLSLEISPQNVDVNVHPTKHEVHFLHEESI-LEV 50 +E YA YL K F+YLSL+SP+DVNVHP+K VHFL+I+Sbjct 287 LEETYAKYLHKGASYFVYLSLNMSPEQLDVNVHPSKRIVHFLYDQEIATSI 337 Final HSPFinal HSP +E YA YL K F+L+SP+DVNVHP+K V +I High-scoring pair(HSP)High-scoring pair(HSP)HFL 18HFV 15 HFS 14HWL 13NFL 13DFL 12HWV 10etc YLS

31、15YLT 12 YVS 12YIT 10etc Neighborhood Neighborhood wordswordsNeighborhood Neighborhood score thresholdscore thresholdT(-f)=11T(-f)=11Query:IETVYAAYLPKNTHPFLYLSLEISPQNVDVNVHPTKHEVHFLHEESILEVexample query wordsexample query wordsNCBI FieldGuideScoring Systems-Nucleotides A G C TA+1 3 3-3G 3+1 3-3C 3 3

32、+1-3T 3 3 3+1Identity matrixCAGGTAGCAAGCTTGCATGTCA|raw score=19-9=10CACGTAGCAAGCTTG-GTGTCA-r 1-q-3 NCBI FieldGuideScoring Systems-ProteinsPosition Independent MatricesPAM Matrices(Percent Accepted Mutation)Derived from observation;small dataset of alignments Implicit model of evolution All calculate

33、d from PAM1 PAM250 widely usedBLOSUM Matrices(BLOck SUbstitution Matrices)Derived from observation;large dataset of highly conserved blocks Each matrix derived separately from blocks with a defined percent identity cutoff BLOSUM62-default matrix for BLASTPosition Specific Score Matrices(PSSMs)PSI-an

34、d RPS-BLASTNCBI FieldGuideA 4R-1 5 N-2 0 6D-2-2 1 6C 0-3-3-3 9Q-1 1 0 0-3 5E-1 0 0 2-4 2 5G 0-2 0-1-3-2-2 6H-2 0 1-1-3 0 0-2 8I-1-3-3-3-1-3-3-4-3 4 L-1-2-3-4-1-2-3-4-3 2 4K-1 2 0-1-3 1 1-2-1-3-2 5M-1-1-2-3-1 0-2-3-2 1 2-1 5F-2-3-3-3-2-3-3-3-1 0 0-3 0 6P-1-2-2-1-3-1-1-2-2-3-3-1-2-4 7S 1-1 1 0-1 0 0 0

35、-1-2-2 0-1-2-1 4T 0-1 0-1-1-1-1-2-2-1-1-1-1-2-1 1 5W-3-3-4-4-2-2-3-2-2-3-2-3-1 1-4-3-2 11Y-2-2-2-3-2-1-2-3 2-1-1-2-1 3-3-2-2 2 7V 0-3-3-3-1-2-2-3-3 3 1-2 1-1-2-2 0-3-1 4X 0-1-1-1-2-1-1-1-1-1-1-1-1-1-2 0 0-2-1-1-1 A R N D C Q E G H I L K M F P S T W Y V XBLOSUM62DFNegative for less likely substitutio

36、nsDYFPositive for more likely substitutionsNCBI FieldGuidePosition-Specific Score MatrixDAF-1Serine/Threonine protein kinases catalytic loop174PSSM scores54NCBI FieldGuide A R N D C Q E G H I L K M F P S T W Y V 435 K -1 0 0-1-2 3 0 3 0-2-2 1-1-1-1-1-1-1-1-2 436 E 0 1 0 2-1 0 2-1 0-1-1 0 0 0-1 0 0-1

37、-1-1 437 S 0 0-1 0 1 1 0 1 1 0-1 0 0 0 2 0-1-1 0-1 438 N -1 0-1-1 1 0-1 3 3-1-1 1-1 0 0-1-1 1 1-1 439 K -2 1 1-1-2 0-1-2-2-1-2 5 1-2-2-1-1-2-2-1 440 P -2-2-2-2-3-2-2-2-2-1-2-1 0-3 7-1-2-3-1-1 441 A 3-2 1-2 0-1 0 1-2-2-2 0-1-2 3 1 0-3-3 0 442 M -3-4-4-4-3-4-4-5-4 7 0-4 1 0-4-4-2-4-1 2 443 A 4-4-4-4 0

38、-4-4-3-4 4-1-4-2-3-4-1-2-4-3 4 444 H -4-2-1-3-5-2-2-4 10-6-5-3-4-3-2-3-4-5 0-5 445 R -4 8-3-4 0-1-2-3-2-5-4 0-3-2-4-3-3 0-4-5 446 D -4-4-1 8-6-2 0-3-3-5-6-3-5-6-4-2-3-7-5-5 447 I -4-5-6-6-3-4-5-6-5 3 5-5 1 1-5-5-3-4-3 1 448 K 0 0 1-3-5-1-1-3-3-5-5 7-4-5-3-1-2-5-4-4 449 S 0-3-2-3 0-2-2-3-3-4-4-2-4-5

39、2 6 2-5-4-4 450 K 0 3 0 1-5 0 0-4-1-4-3 4-3-2 2 1-1-5-4-4 451 N -4-3 8-1-5-2-2-3-1-6-6-2-4-5-4-1-2-6-4-5 452 I -3-5-5-6 0-5-5-6-5 6 2-5 2-2-5-4-3-5-3 3 453 M -4-4-6-6-3-4-5-6-5 0 6-5 1 0-5-4-3-4-3 0 454 V -3-3-5-6-3-4-5-6-5 3 3-4 2-2-5-4-3-5-3 5 455 K -2 1 1 4-5 0-1-2 1-4-2 4-3-2-3 0-1-5-2-3 456 N 1

40、 1 3 0-4-1 1 0-3-4-4 3-2-5-2 2-2-5-4-4 457 D -3-2 5 5-1-1 1-1 0-5-4 0-2-5-1 0-2-6-4-5 458 L -3-1 0-3 0-3-2 3-4-2 3 0 1 1-2-2-3 5-1-3Position-Specific Score Matrixcatalytic loop./blastpgp-i NP_499868.2-d nr-j 3-Q NP_499868.pssm NCBI FieldGuideLocal Alignment StatisticsHigh scores of local alignments

41、between two random sequencesfollow the Extreme Value DistributionScore(S)Alignments(applies to ungapped alignments)E=Kmne-S or E=mn2-SK=scale for search space =scale for scoring system S=bitscore=(S-lnK)/ln2Expect ValueExpect ValueE=number of database hits you expect to find by chance,Syour scoreexp

42、ected number of random hitsMore info:NCBI FieldGuideAdvanced BLAST Options:NucleotideExample Entrez Queriesnucleotide allFilter NOT mammaliaOrganismgreen plantsOrganismbiomol mrnaPropertiesgbdiv estProperties AND ratorganismOther Advancede 10000 expect value-v 2000 descriptions-b 2000 alignmentsNCBI

43、 FieldGuideAdvanced BLAST Options:ProteinMatrix SelectionPAM30-most stringentBLOSUM45-least stringentExample Entrez Queriesproteins allFilter NOT mammaliaOrganismgreen plantsOrganismsrcdb refseqPropertiesOther Advancede 10000 expect value-v 2000 descriptions-b 2000 alignmentsLimit by taxonMus muscul

44、usOrganismMammaliaOrganismViridiplantaeOrganismNCBI FieldGuide sp|P27476|NSR1_YEAST NUCLEAR LOCALIZATION SEQUENCE BINDING PROTEIN(P67)Length=414 Score=40.2 bits(92),Expect=0.013 Identities=35/131(26%),Positives=56/131(42%),Gaps=4/131(3%)Query:362 STTSLTSSSTSGSSDKVYAHQMVRTDSREQKLDAFLQPLSKPLS-SQPQAIVT

45、EDKTD 418 S+S SSS+S SS+S +S S S+E K Sbjct:29 SSSSSESSSSSSSSSESESESESESESSSSSSSSDSESSSSSSSDSESEAETKKEESKDS 88FilteredUnfilteredLow Complexity FilteringNCBI FieldGuideOther BLAST Algorithms MegablastDiscontiguous MegablastPSI-BLASTPHI-BLASTNCBI FieldGuideMegablast:NCBIs Genome Annotator Long alignment

46、s of similar DNA sequencesGreedy algorithmConcatenation of query sequencesFaster than blastn;less sensitiveNCBI FieldGuideMegaBLAST&Word SizeTrade-off:sensitivity vs speed23blastp828megablast711blastnminimumdefaultWORD SIZENCBI FieldGuideDiscontiguous MegablastUses discontiguous word matchesBetter f

47、or cross-species comparisonsNCBI FieldGuideTemplates for Discontiguous WordsW=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,

48、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:111010010110010010111 Reference:Ma,B,Tromp,J,Li,M.PatternHunter:faster and more sensitive homolog

49、y search.Bioinformatics March,2002;18(3):440-5 W=word size;#matches in templatet=template lengthNCBI FieldGuideDiscontiguous(Cross-species)MegaBLASTNCBI FieldGuideDiscontiguous Word OptionsNCBI FieldGuideMegaBLAST vs Discontiguous MegaBLASTNM_017460Homo sapiens cytochrome P450,family 3,subfamily A,p

50、olypeptide 4(CYP3A4),transcript variant 1,mRNA(2768 letters)vs DrosophilaNCBI FieldGuideMegaBLAST vs Discontiguous MegaBLAST MegaBLAST=“No significant similarity found.”Discontiguous megaBLAST=NCBI FieldGuideAnother Example.Discontiguous megaBLAST=numerous hits.Query:NM_078651 Drosophila melanogaste