淀粉樣變性病課件

1、A Field Guide Genome resources Sequence similarity淀粉樣變性病A Field Guide Genome resourGenome ResourcesLocusLinkGene databaseUniGeneTrace ArchiveMap ViewerHomologene淀粉樣變性病Genome ResourcesLocusLinkGene Genomic Biology淀粉樣變性病Genomic Biology淀粉樣變性病淀粉樣變性病淀粉樣變性病淀粉樣變性病淀粉樣變性病淀粉樣變性病淀粉樣變性病Genome Projects: microb淀粉

2、樣變性病Genome Projects: microb淀粉樣變性病淀粉樣變性病淀粉樣變性病淀粉樣變性病淀粉樣變性病Genome ResourcesLocusLinkGene databaseUniGeneTrace ArchiveMap ViewerHomologene淀粉樣變性病Genome ResourcesLocusLinkGene A single query interface to Sequences- RefSeqs- GenBank- HomologeneMaps MapViewerEntrez linksLocusLinkLocusLink will be replaced

3、by Entrez Gene on MARCH 1, 2005. Check Gene FAQ for current information.淀粉樣變性病A single query interface to Entrez GeneLocusLinkA single query interface to Sequences - RefSeqs - GenBank - HomologeneMaps MapViewerEntrez linksEntrez Gene More organisms - all RefSeq genomes Entrez integration淀粉樣變性病Entrez

4、 GeneLocusLinkA single qGsnsym淀粉樣變性病淀粉樣變性病Gsnsym淀粉樣變性病淀粉樣變性病淀粉樣變性病淀粉樣變性病Global Entrez: NADH2nadh247淀粉樣變性病Global Entrez: NADH2nadh247淀粉樣Entrez Gene: NADH226 records淀粉樣變性病Entrez Gene: NADH226 records淀粉Gene Record for Pongo NADH2Homo sapiens淀粉樣變性病Gene Record for Pongo NADH2HomDisplay Exons/Introns: Gen

5、e Table淀粉樣變性病Display Exons/Introns: Gene TGene Table淀粉樣變性病Gene Table淀粉樣變性病A Record With More Data: Human HFE血色沉著病淀粉樣變性病A Record With More Data: HumanGene Graphic LinksNM_NP_淀粉樣變性病Gene Graphic LinksNM_NP_淀粉樣變性病Introns/Exons: Gene Tablelinks to sequence淀粉樣變性病Introns/Exons: Gene TablelinA Record With M

6、ore Data: Human HFE淀粉樣變性病A Record With More Data: HumanEntrez SNPhfegene name AND humanorgn 52血色沉著病淀粉樣變性病Entrez SNPhfegene name AND hLinking to SNP染色體定位基因定位序列定位淀粉樣變性病Linking to SNP染色體定位基因定位序列定位淀粉樣SNP in Structure淀粉樣變性病SNP in Structure淀粉樣變性病Link to OMIM淀粉樣變性病Link to OMIM淀粉樣變性病Variants in OMIM淀粉樣變性病Va

7、riants in OMIM淀粉樣變性病Genome ResourcesLocusLinkGene databaseTrace ArchiveMap ViewerHomologeneUniGene淀粉樣變性病Genome ResourcesLocusLinkGene Gene-oriented clusters of expressed sequences Automatic clustering using MegaBlast Each cluster represents a unique gene Informed by genome hits Information on tissue

8、 types and map locations Useful for gene discovery and selection of mapping reagentsUniGene淀粉樣變性病Gene-oriented clusters of exprA Cluster of ESTsquery5 EST hits3 EST hits淀粉樣變性病A Cluster of ESTsquery5 EST hUnigene淀粉樣變性病Unigene淀粉樣變性病UniGene Collections淀粉樣變性病UniGene Collections淀粉樣變性病Example UniGene Clus

9、ter淀粉樣變性病Example UniGene Cluster淀粉樣變性病Histogram of cluster sizes for UniGene Hs build 177淀粉樣變性病Histogram of cluster sizes forUniGene Cluster Hs.95351淀粉樣變性病UniGene Cluster Hs.95351淀粉樣變性病UniGene Cluster Hs.95351淀粉樣變性病UniGene Cluster Hs.95351淀粉樣變性病UniGene Cluster Hs.95351: expression淀粉樣變性病UniGene Clust

10、er Hs.95351: exprUniGene Cluster Hs.95351: seqs淀粉樣變性病UniGene Cluster Hs.95351: seqsDownload sequencesweb page淀粉樣變性病Download sequencesweb page淀粉樣變Genome ResourcesLocusLinkGene databaseUniGeneTrace ArchiveMap ViewerHomologene淀粉樣變性病Genome ResourcesLocusLinkGene The New HomologeneAutomated detection of

11、homologs among the annotated genes of completely sequenced eukaryotic genomes. No longer UniGene basedProtein similarities firstGuided by taxonomic treeIncludes orthologs and paralogs淀粉樣變性病The New HomologeneAutomated de 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

12、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。淀粉樣變性病 Orthologs 和 Paralogsgene duplicationParalogs vs Orthologsearly globin geneA-chain gene B-chain genefrog A chick A mouse Amouse B chick B frog Bparalogsorthologs orthologs淀粉樣變性病gene duplicationParalogs vs OrT

13、he New Homologene Homologene Build 37.2Species Number of genes input grouped groups淀粉樣變性病The New Homologene RAG1 Homologenerag112recombination activating gene 淀粉樣變性病RAG1 Homologenerag112recombiRAG1 HomolgeneRAG1Amniota 淀粉樣變性病RAG1 HomolgeneRAG1Amniota Homolgene: RAG1淀粉樣變性病Homolgene: RAG1淀粉樣變性病淀粉樣變性病淀

14、粉樣變性病Homolgene: RAG1淀粉樣變性病Homolgene: RAG1淀粉樣變性病Genome ResourcesLocusLinkGene databaseUniGeneTrace ArchiveMap ViewerHomologene淀粉樣變性病Genome ResourcesLocusLinkGene 淀粉樣變性病淀粉樣變性病淀粉樣變性病淀粉樣變性病淀粉樣變性病淀粉樣變性病MapViewer淀粉樣變性病MapViewer淀粉樣變性病List View淀粉樣變性病List View淀粉樣變性病Human MapVieweradar腺甙脫氨酶淀粉樣變性病Human MapView

15、eradar腺甙脫氨酶淀粉樣變性病MapViewer: Human ADAR4淀粉樣變性病MapViewer: Human ADAR4淀粉樣變性病MV Hs ADAR3 UTR5 UTR淀粉樣變性病MV Hs ADAR3 UTR5 UTR淀粉樣變性病Maps & Options-Sequence maps-Ab initioAssemblyRepeatsBES_CloneCloneNCI_CloneContigComponentCpG islanddbSNP haplotypeFosmidGenBank_DNAGenePhenotypeSAGE_TagSTSTCAG_RNATranscript

16、 (RNA)Hs_UniGeneHs_EST-Cytogenetic maps-IdeogramFISH CloneGene_CytogeneticMitelman BreakpointMorbid/Disease-Genetic Maps-deCODEGenethonMarshfield-RH maps-GeneMap99-G3GeneMap99-GB4NCBI RHStandford-G3TNGWhitehead-RHWhitehead-YACMm_UniGeneMm_ESTRn_UniGeneRn_ESTSsc_UniGeneSsc_ESTBt_UniGeneBt_ESTGga_UniG

17、eneGga_ESTVariationMaps & Options= SNP淀粉樣變性病Maps & Options-Sequence maps-MapViewerUniGeneComponentRepeatsGene淀粉樣變性病MapViewerUniGeneComponentRepeaMaster map: repeats淀粉樣變性病Master map: repeats淀粉樣變性病GenePhenotypeVariation淀粉樣變性病GenePhenotypeVariation淀粉樣變性病Maps & OptionsMaps & Options淀粉樣變性病Maps & OptionsM

18、aps & Options淀粉Genome ResourcesLocusLinkGene databaseUniGeneTrace ArchiveMap ViewerHomologene淀粉樣變性病Genome ResourcesLocusLinkGene 淀粉樣變性病淀粉樣變性病淀粉樣變性病淀粉樣變性病Strongylocentrotus purpuratus Traces淀粉樣變性病Strongylocentrotus purpuratus BLASTBasic Local Alignment Search Tool淀粉樣變性病BLASTBasic Local Alignment SeaW

19、eb AccessBLASTVASTEntrezTextSequenceStructure淀粉樣變性病Web AccessBLASTVASTEntrezTextS淀粉樣變性病淀粉樣變性病Basic Local Alignment Search Tool Why use sequence similarity? BLAST algorithm BLAST statistics BLAST output Examples淀粉樣變性病Basic Local Alignment Search TWhy Do We Need Sequence Similarity Searching?To identi

20、fy and annotate sequencesTo evaluate evolutionary relationshipsOther:model genomic structure (e.g., Spidey)check primer specificity in silico: NCBIs tool淀粉樣變性病Why Do We Need Sequence SimilBLAST Website Stats淀粉樣變性病BLAST Website Stats淀粉樣變性病Global vs Local AlignmentSeq 1Seq 2Seq 1Seq 2Global alignmentL

21、ocal alignment淀粉樣變性病Global vs Local AlignmentSeq 1Global vs Local AlignmentSeq1: WHEREISWALTERNOW (16aa)Seq2: HEWASHEREBUTNOWISHERE (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 21淀

22、粉樣變性病Global vs Local AlignmentSeq1:The Flavors of BLASTStandard BLASTtraditional “contiguous” word hitposition independent scoring nucleotide, protein and translations (blastn, blastp, blastx, tblastn, tblastx)Megablastoptimized for large batch searchescan use discontiguous wordsPSI-BLASTconstructs

23、PSSMs automatically; uses as queryvery sensitive protein searchRPS BLASTsearches a database of PSSMstool for conserved domain searches淀粉樣變性病The Flavors of BLASTStandard BWidely used similarity search toolHeuristic approach based on Smith Waterman algorithmFinds best local alignmentsProvides statisti

24、cal significanceAll combinations (DNA/Protein) query and database.DNA vs DNA blastnDNA translation vs Protein blastxProtein vs Protein blastpProtein vs DNA translation tblastnDNA translation vs DNA translation tblastx www, standalone, and network clientsBasic Local Alignment Search Tool淀粉樣變性病Widely

25、used similarity search Translated BLASTQueryDatabaseProgramNPucleotideroteinNNNNPPblastxtblastntblastxPPPPPPPPPPPPPPPPPPPPPPPPParticularly useful for nucleotide sequences withoutprotein annotations, such as ESTs or genomic DNA淀粉樣變性病Translated BLASTQueryDatabasePHow BLAST WorksMake lookup table of “w

26、ords” for queryScan database for hitsUngapped extensions of hits (initial HSPs)Gapped extensions (no traceback)Gapped extensions (traceback; alignment details)淀粉樣變性病How BLAST WorksMake lookup tabNucleotide WordsGTACTGGACATGGACCCTACAGGAAQuery:GTACTGGACAT TACTGGACATG ACTGGACATGG CTGGACATGGA TGGACATGGA

27、C GGACATGGACC GACATGGACCC ACATGGACCCTMake a lookuptable of words11-mer. . .828megablast711blastnminimumdefaultWORD SIZE淀粉樣變性病Nucleotide WordsGTACTGGACATGGAProtein WordsGTQITVEDLFYNIATRRKALKNQuery: Neighborhood WordsLTV, MTV, ISV, LSV, etc.GTQ TQI QIT ITV TVE VED EDL DLF .Make a lookuptable of wordsW

28、ord size = 3 (default)Word size can only be 2 or 3 -f 11 = blastp default 淀粉樣變性病Protein WordsGTQITVEDLFYNIATRRMinimum Requirements for a Hit Nucleotide BLAST requires one exact match Protein BLAST requires two neighboring matches within 40 aaGTQITVEDLFYNI SEI YYNATCGCCATGCTTAATTGGGCTT CATGCTTAATT ne

29、ighborhood wordsone exact matchtwo matches -A 40 = blastp default 淀粉樣變性病Minimum Requirements for a HitBLASTP Summary YLS HFLSbjct 287 LEETYAKYLHKGASYFVYLSLNMSPEQLDVNVHPSKRIVHFLYDQEI 333 Query 1 IETVYAAYLPKNTHPFLYLSLEISPQNVDVNVHPTKHEVHFLHEESI 47Gapped extension with trace backQuery 1 IETVYAAYLPKNTHPF

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

31、borhood wordsNeighborhood score thresholdT (-f) =11Query: IETVYAAYLPKNTHPFLYLSLEISPQNVDVNVHPTKHEVHFLHEESILEVexample query words淀粉樣變性病BLASTP Summary Scoring Systems - Nucleotides A G C TA +1 3 3 -3G 3 +1 3 -3C 3 3 +1 -3T 3 3 3 +1Identity matrixCAGGTAGCAAGCTTGCATGTCA| | | raw score = 19-9 = 10CACGTAGC

32、AAGCTTG-GTGTCA -r 1 -q -3 淀粉樣變性病Scoring Systems - Nucleotides Scoring Systems - ProteinsPosition Independent MatricesPAM Matrices (Percent Accepted Mutation) Derived from observation; small dataset of alignments Implicit model of evolution All calculated from PAM1 PAM250 widely usedBLOSUM Matrices (

33、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- and RPS-BLAST淀粉樣變性病Scoring Systems - Prote

34、insPosiA 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 -

35、1 -2 -2 -1 -3 -1 -1 -2 -2 -3 -3 -1 -2 -4 7S 1 -1 1 0 -1 0 0 0 -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

36、 -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 substitutionsDYFPositive for more likely substitutions淀粉樣變性病A 4BLOSUM62DFNegative for lesPosition-Specific Score MatrixDAF-1Serine/Threonine protein kinases catalytic l

37、oop174PSSM scores54淀粉樣變性病Position-Specific Score Matrix 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 -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

38、 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 -4 -4 -3 -4 4 -1 -4 -2

39、-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 -

40、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 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 -

41、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 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

42、-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 淀粉樣變性病 A R N D C Q ELocal Alignment StatisticsHigh scores of local alignments between two random sequencesfollow the Extreme Value DistributionScore (S)Alignments(ap

43、plies to ungapped alignments)E = Kmne-S or E = mn2-SK = scale for search space = scale for scoring system S = bitscore = (S - lnK)/ln2Expect ValueE = number of database hits you expect to find by chance, Syour scoreexpected number of random hitsMore info: 淀粉樣變性病Local Alignment StatisticsHighAdvanced

44、 BLAST Options: NucleotideExample Entrez Queriesnucleotide allFilter NOT mammaliaOrganismgreen plantsOrganismbiomol mrnaPropertiesgbdiv estProperties AND ratorganismOther Advancede 10000 expect value-v 2000 descriptions-b 2000 alignments淀粉樣變性病Advanced BLAST Options: NucleoAdvanced BLAST Options: Pro

45、teinMatrix SelectionPAM30 - most stringentBLOSUM45 - least stringentExample Entrez Queriesproteins allFilter NOT mammaliaOrganismgreen plantsOrganismsrcdb refseqPropertiesOther Advancede 10000 expect value-v 2000 descriptions-b 2000 alignmentsLimit by taxonMus musculusOrganismMammaliaOrganismViridip

46、lantaeOrganism淀粉樣變性病Advanced BLAST Options: Protei 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 STTSLTSSSTSGSSDKVYAHQMVRTDSREQKLDAFLQPLSKPL

47、SSQPQAIVTEDKTD 418 S+S SSS+S SS + + +S + + S S S+ + E K Sbjct: 29 SSSSSESSSSSSSSSESESESESESESSSSSSSSDSESSSSSSSDSESEAETKKEESKDS 88FilteredUnfilteredLow Complexity Filtering淀粉樣變性病 sp|P27476|NSR1_YEAST NUCLEAR Other BLAST Algorithms MegablastDiscontiguous MegablastPSI-BLASTPHI-BLAST淀粉樣變性病Other BLAST Al

48、gorithms MegablaMegablast: NCBIs Genome Annotator Long alignments of similar DNA sequencesGreedy algorithmConcatenation of query sequencesFaster than blastn; less sensitive淀粉樣變性病Megablast: NCBIs Genome AnnotMegaBLAST & Word SizeTrade-off: sensitivity vs speed23blastp828megablast711blastnminimumdefau

49、ltWORD SIZE淀粉樣變性病MegaBLAST & Word SizeTrade-offDiscontiguous MegablastUses discontiguous word matchesBetter for cross-species comparisons淀粉樣變性病Discontiguous MegablastUses diTemplates for Discontiguous WordsW = 11, t = 16, coding: 1101101101101101W = 11, t = 16, non-coding: 1110010110110111W = 12, t

50、= 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 = 1

51、1, 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 homology search. Bioinformatics March, 2002; 18(3):440-5 W = word size; # matches in

52、templatet = template length淀粉樣變性病Templates for Discontiguous WoDiscontiguous (Cross-species) MegaBLAST淀粉樣變性病Discontiguous (Cross-species) Discontiguous Word Options淀粉樣變性病Discontiguous Word Options淀粉樣變MegaBLAST vs Discontiguous MegaBLASTNM_017460Homo sapiens cytochrome P450, family 3, subfamily A, po

53、lypeptide 4 (CYP3A4), transcript variant 1, mRNA (2768 letters) vs Drosophila淀粉樣變性病MegaBLAST vs Discontiguous MegMegaBLAST vs Discontiguous MegaBLAST MegaBLAST = “No significant similarity found.” Discontiguous megaBLAST =淀粉樣變性病MegaBLAST vs Discontiguous MegAnother Example . . . Discontiguous megaBL

54、AST = numerous hits . . .Query: NM_078651 Drosophila melanogaster CG18582-PA (mbt) mRNA, (3244 bp)/note= mushroom bodies tiny; synonyms: Pak2, STE20, dPAK2 MegaBLAST = “No significant similarity found.”Database: nr (nt), Mammaliaorgn淀粉樣變性病Another Example . . . DiscontiEx: Discontiguous MegaBLAST淀粉樣變

55、性病Ex: Discontiguous MegaBLAST淀粉Ex: BLASTN淀粉樣變性病Ex: BLASTN淀粉樣變性病PSI-BLASTExample: Confirming relationships of purinenucleotide metabolism proteinsPosition-specific Iterated BLAST淀粉樣變性病PSI-BLASTExample: Confirming gi|113340|sp|P03958|ADA_MOUSE ADENOSINE DEAMINASE (ADENOSINEMAQTPAFNKPKVELHVHLDGAIKPETIL

56、YFGKKRGIALPADTVEELRNIIGMDKPLSLPGFVIAGCREAIKRIAYEFVEMKAKEGVVYVEVRYSPHLLANSKVDPMPWNQTEGDVTPDDVVDEQAFGIKVRSILCCMRHQPSWSLEVLELCKKYNQKTVVAMDLAGDETIEGSSLFPGHVEAYRTVHAGEVGSPEVVREAVDILKTERVGHGYHTIEDEALYNRLLKENMHFEVCPWSSYLTGAVRFKNDKANYSLNTDDPLIFKSTLDTDYQMTKKDMGFTEEEFKRLNINAAKSSFLPEEEKKPSI-BLAST0.005E value c

57、utoff for PSSM淀粉樣變性病gi|113340|sp|P03958|ADA_MOUSERESULTS: Initial BLASTPSame results as protein-protein BLAST; different format淀粉樣變性病RESULTS: Initial BLASTPSame reResults of First PSSM SearchOther purine nucleotide metabolizing enzymes not found by ordinary BLAST淀粉樣變性病Results of First PSSM SearchOtT

58、enth PSSM Search: ConvergenceJust below threshold, another nucleotide metabolism enzymeCheck to add to PSSM淀粉樣變性病Tenth PSSM Search: ConvergenceReverse PSI-BLAST (RPS)-BLAST淀粉樣變性病Reverse PSI-BLAST (RPS)-BLAST淀Adenosine/AMP Deaminase DomainAMP Deaminases.淀粉樣變性病Adenosine/AMP Deaminase DomainPHI-BLASTgi

59、|231729|sp|P30429|CED4_CAEEL CELL DEATH PROTEIN 4MLCEIECRALSTAHTRLIHDFEPRDALTYLEGKNIFTEDHSELISKMSTRLERIANFLRIYRRQASELIDFFNYNNQSHLADFLEDYIDFAINEPDLLRPVVIAPQFSRQMLDRKLLLGNVPKQMTCYIREYHVIKKLDEMCDLDSFFLFLHGRAGSGKSVIASQALSKSDQLIGINYDSIVWLKDSGTAPKSTFDLFTDILKSEDDLLNFPSVEHVTSVVLKRMICNALIDRPNTLFVFDDVVQEETIRWAQELRLRCLVTTRDVEIASQTCEFIEVTSLEIDECYDFLEAYGMPMPVGEKEEDVLNKTIELSSGNPATLMMFFKSCEPKTFEKGAxxxxGKST淀粉樣變性病PHI-BLASTgi|231729|sp|P30429|Whats New?淀粉樣變性病Whats New?淀粉樣變性病BLAST DatabasesNucleotiderefseq_rna = NM_*, XM_*refseq_genomic = NC_*, NG_*env_ntenvironmental samplefilter, e.g., 16S rRNAProtei