淀粉样变性病ppt课件

A Field Guide Genome resources Sequence similarity淀粉样变性病A Field Guide Genome resour1Genome ResourcesLocusLinkLocusLinkLocusLinkLocusLinkGene databaseGene databaseGene databaseGene databaseUniGeneUniGeneUniGeneUniGeneTrace ArchiveTrace ArchiveTrace ArchiveTrace ArchiveMap ViewerMap ViewerMap ViewerMap ViewerHomologeneHomologeneHomologeneHomologene淀粉样变性病Genome ResourcesLocusLinkGene 2Genomic Biology淀粉样变性病Genomic Biology淀粉样变性病3淀粉样变性病淀粉样变性病4淀粉样变性病淀粉样变性病5淀粉样变性病淀粉样变性病6Genome Projects:microb淀粉样变性病Genome Projects:microb淀粉样变性病7淀粉样变性病淀粉样变性病8淀粉样变性病淀粉样变性病9Genome ResourcesLocusLinkLocusLinkLocusLinkLocusLinkGene databaseGene databaseGene databaseGene databaseUniGeneUniGeneUniGeneUniGeneTrace ArchiveTrace ArchiveTrace ArchiveTrace ArchiveMap ViewerMap ViewerMap ViewerMap ViewerHomologeneHomologeneHomologeneHomologene淀粉样变性病Genome ResourcesLocusLinkGene 10A single query interface to SequencesSequences-RefSeqs-RefSeqs-GenBank-GenBank-Homologene-HomologeneMaps MapViewerMaps MapViewerEntrez linksEntrez linksLocusLinkLocusLink will be replaced by Entrez Gene on MARCH 1,2005.Check Gene FAQ for current information.淀粉样变性病A single query interface to 11Entrez GeneLocusLinkA single query interface to SequencesSequences -RefSeqs -RefSeqs -GenBank -GenBank -Homologene -HomologeneMaps MapViewerMaps MapViewerEntrez linksEntrez linksEntrez GeneMore organisms-all RefSeq genomes Entrez integration淀粉样变性病Entrez GeneLocusLinkA single q12Gsnsym淀粉样变性病淀粉样变性病Gsnsym淀粉样变性病淀粉样变性病13淀粉样变性病淀粉样变性病14Global Entrez:NADH2nadh247淀粉样变性病Global Entrez:NADH2nadh247淀粉样15Entrez Gene:NADH226 records淀粉样变性病Entrez Gene:NADH226 records淀粉16Gene Record for Pongo NADH2Homo sapiens淀粉样变性病Gene Record for Pongo NADH2Hom17Display Exons/Introns:Gene Table淀粉样变性病Display Exons/Introns:Gene T18Gene Table淀粉样变性病Gene Table淀粉样变性病19A Record With More Data:Human HFE血色沉着病淀粉样变性病A Record With More Data:Human20Gene Graphic LinksNM_NM_NP_NP_淀粉样变性病Gene Graphic LinksNM_NP_淀粉样变性病21Introns/Exons:Gene Tablelinks to sequence淀粉样变性病Introns/Exons:Gene Tablelin22A Record With More Data:Human HFE淀粉样变性病A Record With More Data:Human23Entrez SNPhfegene name AND humanorgn 52血色沉着病淀粉样变性病Entrez SNPhfegene name AND h24Linking to SNP染色体定位基因定位序列定位淀粉样变性病Linking to SNP染色体定位基因定位序列定位淀粉样25SNP in Structure淀粉样变性病SNP in Structure淀粉样变性病26Link to OMIM淀粉样变性病Link to OMIM淀粉样变性病27Variants in OMIM淀粉样变性病Variants in OMIM淀粉样变性病28Genome ResourcesLocusLinkLocusLinkLocusLinkLocusLinkGene databaseGene databaseGene databaseGene databaseTrace ArchiveTrace ArchiveTrace ArchiveTrace ArchiveMap ViewerMap ViewerMap ViewerMap ViewerHomologeneHomologeneHomologeneHomologeneUniGeneUniGene淀粉样变性病Genome ResourcesLocusLinkGene 29Gene-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 locations Useful for gene discovery and selection of mapping reagentsUniGene淀粉样变性病Gene-oriented clusters of expr30A Cluster of ESTsquery5 EST hits3 EST hits淀粉样变性病A Cluster of ESTsquery5 EST h31Unigene淀粉样变性病Unigene淀粉样变性病32UniGene Collections淀粉样变性病UniGene Collections淀粉样变性病33Example UniGene Cluster淀粉样变性病Example UniGene Cluster淀粉样变性病34Histogram of cluster sizes for UniGene Hs build 177淀粉样变性病Histogram of cluster sizes for35UniGene Cluster Hs.95351淀粉样变性病UniGene Cluster Hs.95351淀粉样变性病36UniGene Cluster Hs.95351淀粉样变性病UniGene Cluster Hs.95351淀粉样变性病37UniGene Cluster Hs.95351:expression淀粉样变性病UniGene Cluster Hs.95351:expr38UniGene Cluster Hs.95351:seqs淀粉样变性病UniGene Cluster Hs.95351:seqs39Download sequencesweb page淀粉样变性病Download sequencesweb page淀粉样变40Genome ResourcesLocusLinkLocusLinkLocusLinkLocusLinkGene databaseGene databaseGene databaseGene databaseUniGeneUniGeneUniGeneUniGeneTrace ArchiveTrace ArchiveTrace ArchiveTrace ArchiveMap ViewerMap ViewerMap ViewerMap ViewerHomologeneHomologeneHomologeneHomologene淀粉样变性病Genome ResourcesLocusLinkGene 41The New HomologeneAutomated detection of homologs among the annotated genes of completely sequenced eukaryotic genomes.No longer UniGene basedProtein similarities firstGuided by taxonomic treeIncludes orthologs and paralogs淀粉样变性病The New HomologeneAutomated de42Orthologs 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。淀粉样变性病 Orthologs 和 Paralogs43gene duplicationParalogs vs Orthologsearly globin geneA-chain gene B-chain genefrog A chick A mouse Amouse B chick B frog Bparalogsorthologs orthologs淀粉样变性病gene duplicationParalogs vs Or44The New HomologeneHomologene Build 37.2Species Number of genes input grouped groups淀粉样变性病The New Homologene 45RAG1 Homologenerag112recombination activating gene 淀粉样变性病RAG1 Homologenerag112recombi46RAG1 HomolgeneRAG1Amniota 淀粉样变性病RAG1 HomolgeneRAG1Amniota 47Homolgene:RAG1淀粉样变性病Homolgene:RAG1淀粉样变性病48淀粉样变性病淀粉样变性病49Homolgene:RAG1淀粉样变性病Homolgene:RAG1淀粉样变性病50Genome ResourcesLocusLinkLocusLinkLocusLinkLocusLinkGene databaseGene databaseGene databaseGene databaseUniGeneUniGeneUniGeneUniGeneTrace ArchiveTrace ArchiveTrace ArchiveTrace ArchiveMap ViewerMap ViewerMap ViewerMap ViewerHomologeneHomologeneHomologeneHomologene淀粉样变性病Genome ResourcesLocusLinkGene 51淀粉样变性病淀粉样变性病52淀粉样变性病淀粉样变性病53淀粉样变性病淀粉样变性病54MapViewer淀粉样变性病MapViewer淀粉样变性病55List View淀粉样变性病List View淀粉样变性病56Human MapVieweradar腺甙脱氨酶淀粉样变性病Human MapVieweradar腺甙脱氨酶淀粉样变性病57MapViewer:Human ADAR4淀粉样变性病MapViewer:Human ADAR4淀粉样变性病58MV Hs ADAR3 UTR5 UTR淀粉样变性病MV Hs ADAR3 UTR5 UTR淀粉样变性病59Maps&Options-Sequence mapsSequence maps-Ab initioAssemblyRepeatsBES_CloneCloneNCI_CloneContigComponentCpG islanddbSNP haplotypeFosmidGenBank_DNAGenePhenotypeSAGE_TagSTSTCAG_RNATranscript(RNA)Hs_UniGeneHs_EST-Cytogenetic mapsCytogenetic 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_UniGeneGga_ESTVariationMaps&Options=SNP淀粉样变性病Maps&Options-Sequence maps-60MapViewerUniGeneComponentRepeatsGene淀粉样变性病MapViewerUniGeneComponentRepea61Master map:repeats淀粉样变性病Master map:repeats淀粉样变性病62GenePhenotypeVariation淀粉样变性病GenePhenotypeVariation淀粉样变性病63Maps&OptionsMaps&Options淀粉样变性病Maps&OptionsMaps&Options淀粉64Genome ResourcesLocusLinkLocusLinkLocusLinkLocusLinkGene databaseGene databaseGene databaseGene databaseUniGeneUniGeneUniGeneUniGeneTrace ArchiveTrace ArchiveTrace ArchiveTrace ArchiveMap ViewerMap ViewerMap ViewerMap ViewerHomologeneHomologeneHomologeneHomologene淀粉样变性病Genome ResourcesLocusLinkGene 65淀粉样变性病淀粉样变性病66淀粉样变性病淀粉样变性病67Strongylocentrotus purpuratus Traces淀粉样变性病Strongylocentrotus purpuratus 68BLASTBasic Local Alignment Search Tool淀粉样变性病BLASTBasic Local Alignment Sea69Web AccessBLASTVASTEntrezTextSequenceStructure淀粉样变性病Web AccessBLASTVASTEntrezTextS70淀粉样变性病淀粉样变性病71Basic Local Alignment Search ToolWhy use sequence similarity?BLAST algorithm BLAST statistics BLAST output Examples淀粉样变性病Basic Local Alignment Search T72Why Do We Need Sequence Similarity Searching?To identify and annotate sequencesTo evaluate evolutionary relationshipsOther:model genomic structure(e.g.,Spidey)check primer specificity in silico:NCBIs tool淀粉样变性病Why Do We Need Sequence Simil73BLAST Website Stats淀粉样变性病BLAST Website Stats淀粉样变性病74Global vs Local AlignmentSeq 1Seq 2Seq 1Seq 2Global alignmentLocal alignment淀粉样变性病Global vs Local AlignmentSeq 175Global 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淀粉样变性病Global vs Local AlignmentSeq1:76The 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 PSSMs automatically;uses as queryvery sensitive protein searchRPS BLASTsearches a database of PSSMstool for conserved domain searches淀粉样变性病The Flavors of BLASTStandard B77Widely used similarity 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 translation vs DNA translation tblastx www,standalone,and network clientsBasic Local Alignment Search Tool淀粉样变性病Widely used similarity search 78Translated BLASTQueryQueryDatabaseDatabaseProgramProgramNPucleotideroteinNNNNPPblastxtblastntblastxPPPPPPPPPPPPPPPPPPPPPPPPParticularly useful for nucleotide sequences withoutprotein annotations,such as ESTs or genomic DNA淀粉样变性病Translated BLASTQueryDatabaseP79How 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)淀粉样变性病How BLAST WorksMake lookup tab80Nucleotide WordsGTACTGGACATGGACCCTACAGGAAQuery:GTACTGGACAT TACTGGACATG ACTGGACATGG CTGGACATGGA TGGACATGGAC GGACATGGACC GACATGGACCC ACATGGACCCTMake a lookuptable of words11-mer.828megablast711blastnminimumdefaultWORD SIZE淀粉样变性病Nucleotide WordsGTACTGGACATGGA81Protein WordsGTQITVEDLFYNIATRRKALKNQuery:Neighborhood WordsLTV,MTV,ISV,LSV,etc.GTQ TQI QIT ITV TVE VED EDL DLF .Make a lookuptable of wordsWord size=3(default)Word size can only be 2 or 3-f 11=blastp default 淀粉样变性病Protein WordsGTQITVEDLFYNIATRR82Minimum Requirements for a Hit Nucleotide BLAST requires one exact match Protein BLAST requires two neighboring matches within 40 aaGTQITVEDLFYNI SEI YYNATCGCCATGCTTAATTGGGCTT CATGCTTAATT neighborhood wordsone exact matchtwo matches-A 40=blastp default 淀粉样变性病Minimum Requirements for a Hit83BLASTP Summary YLS HFLSbjct 287 LEETYAKYLHKGASYFVYLSLNMSPEQLDVNVHPSKRIVHFLYDQEI 333 Query 1 IETVYAAYLPKNTHPFLYLSLEISPQNVDVNVHPTKHEVHFLHEESI 47Gapped extension with trace backGapped extension with trace backQuery 1 IETVYAAYLPKNTHPFLYLSLEISPQNVDVNVHPTKHEVHFLHEESI-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 15YLT 12 YVS 12YIT 10etc Neighborhood Neighborhood wordswordsNeighborhood Neighborhood score thresholdscore thresholdT(-f)=11T(-f)=11Query:IETVYAAYLPKNTHPFLYLSLEISPQNVDVNVHPTKHEVHFLHEESILEVexample query wordsexample query words淀粉样变性病BLASTP Summary 84Scoring 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=10CACGTAGCAAGCTTG-GTGTCA-r 1-q-3 淀粉样变性病Scoring Systems-Nucleotides 85Scoring 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(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淀粉样变性病Scoring Systems-ProteinsPosi86A 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 0-1-2-2 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 substitutionsDYFPositive for more likely substitutions淀粉样变性病A 4BLOSUM62DFNegative for les87Position-Specific Score MatrixDAF-1Serine/Threonine protein kinases catalytic loop174PSSM scores54淀粉样变性病Position-Specific Score Matrix88 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 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 4-1-4-2-3-4-1-2-4-3 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 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 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 淀粉样变性病 A R N D C Q E89Local Alignment StatisticsHigh scores of local alignments 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 scoreexpected number of random hitsMore info:淀粉样变性病Local Alignment StatisticsHigh90Advanced BLAST Options:NucleotideExample Entrez Queriesnucleotide allFilter NOT mammaliaOrganismgreen plantsOrganismbiomol mrnaPropertiesgbdiv estProperties AND ratorganismOther Advancede 10000 expect value-v 2000 descriptions-b 2000 alignments淀粉样变性病Advanced BLAST Options:Nucleo91Advanced 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 musculusOrganismMammaliaOrganismViridiplantaeOrganism淀粉样变性病Advanced BLAST Options:Protei92 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-SQPQAIVTEDKTD 418 S+S SSS+S SS+S +S S S+E K Sbjct:29 SSSSSESSSSSSSSSESESESESESESSSSSSSSDSESSSSSSSDSESEAETKKEESKDS 88FilteredUnfilteredLow Complexity Filtering淀粉样变性病 sp|P27476|NSR1_YEAST NUCLEAR 93Other BLAST Algorithms MegablastDiscontiguous MegablastPSI-BLASTPHI-BLAST淀粉样变性病Other BLAST Algorithms Megabla94Megablast:NCBIs Genome Annotator Long alignments of similar DNA sequencesGreedy algorithmConcatenation of query sequencesFaster than blastn;less sensitive淀粉样变性病Megablast:NCBIs Genome Annot95MegaBLAST&Word SizeTrade-off:sensitivity vs speed23blastp828megablast711blastnminimumdefaultWORD SIZE淀粉样变性病MegaBLAST&Word SizeTrade-off96Discontiguous MegablastUses discontiguous word matchesBetter for cross-species comparisons淀粉样变性病Discontiguous MegablastUses di97Templates 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,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 homology search.Bioinformatics March,2002;18(3):440-5 W=word size;#matches in templatet=template length淀粉样变性病Templates for Discontiguous Wo98Discontiguous(Cross-species)MegaBLAST淀粉样变性病Discontiguous(Cross-species)99Discontiguous Word Options淀粉样变性病Discontiguous Word Options淀粉样变100MegaBLAST vs Discontiguous MegaBLASTNM_017460Homo sapiens cytochrome P450,family 3,subfamily A,polypeptide 4(CYP3A4),transcript variant 1,mRNA(2768 letters)vs Drosophila淀粉样变性病MegaBLAST vs Discontiguous Meg101MegaBLAST vs Discontiguous MegaBLASTMegaBLAST=“No significant similarity found.”Discontiguous megaBLAST=淀粉样变性病MegaBLAST vs Discontiguous Meg102Another Example.Discontiguous megaBLAST=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淀粉样变性病Another Example.Disconti103Ex:Discontiguous MegaBLAST淀粉样变性病Ex:Discontiguous MegaBLAST淀粉104Ex:BLASTN淀粉样变性病Ex:BLASTN淀粉样变性病105PSI-BLASTExample:Confirming relationships of purinenucleotide metabolism proteinsPosition-specific Iterated BLAST淀粉样变性病PSI-BLASTExample:Confirming 106gi|113340|sp|P03958|ADA_MOUSE ADENOSINE DEAMINASE(ADENOSINEMAQTPAFNKPKVELHVHLDGAIKPETILYFGKKRGIALPADTVEELRNIIGMDKPLSLPGFVIAGCREAIKRIAYEFVEMKAKEGVVYVEVRYSPHLLANSKVDPMPWNQTEGDVTPDDVVDEQAFGIKVRSILCCMRHQPSWSLEVLELCKKYNQKTVVAMDLAGDETIEGSSLFPGHVEAYRTVHAGEVGSPEVVREAVDILKTERVGHGYHTIEDEALYNRLLKENMHFEVCPWSSYLTGAVRFKNDKANYSLNTDDPLIFKSTLDTDYQMTKKDMGFTEEEFKRLNINAAKSSFLPEEEKKPSI-BLAST0.005E value cutoff for PSSM淀粉样变性病gi|113340|sp|P03958|ADA_MOUSE107RESULTS:Initial BLASTPSame results as protein-protein BLAST;different format淀粉样变性病RESULTS:Initial BLASTPSame re108Results of First PSSM SearchOther purine nucleotide metabolizing enzymes not found by ordinary BLAST淀粉样变性病Results of First PSSM SearchOt109Tenth PSSM Search:ConvergenceJust below threshold,another nucleotide metabolism enzymeCheck to add to PSSM淀粉样变性病Tenth PSSM Search:Convergence110Reverse PSI-BLAST(RPS)-BLAST淀粉样变性病Reverse PSI-BLAST(RPS)-BLAST淀111Adenosine/AMP Deaminase DomainAMP Deaminases.淀粉样变性病Adenosine/AMP Deaminase Domain112PHI-BLASTgi|231729|sp|P30429|CED4_CAEEL CELL DEATH PROTEIN 4MLCEIECRALSTAHTRLIHDFEPRDALTYLEGKNIFTEDHSELISKMSTRLERIANFLRIYRRQASELIDFFNYNNQSHLADFLEDYIDFAINEPDLLRPVVIAPQFSRQMLDRKLLLGNVPKQMTCYIREYHVIKKLDEMCDLDSFFLFLHGRAGSGKSVIASQALSKSDQLIGINYDSIVWLKDSGTAPKSTFDLFTDILKSEDDLLNFPSVEHVTSVVLKRMICNALIDRPNTLFVFDDVVQEETIRWAQELRLRCLVTTRDVEIASQTCEFIEVTSLEIDECYDFLEAYGMPMPVGEKEEDVLNKTIELSSGNPATLMMFFKSCEPKTFEKGAxxxxGKST淀粉样变性病PHI-BLASTgi|231729|sp|P30429|113Whats Whats New?New?淀粉样变性病Whats New?淀粉样变性病114BLAST DatabasesNucleotiderefseq_rna=NM_*,XM_*refseq_genomic=NC_*,NG_*env_ntenvironmental samplefilter,e.g.,16S rRNAProteinrefseq=NP_*,XP_*env_nr淀粉样变性病BLAST DatabasesNucleotide淀粉样变性115New FormatterSelect lower caseSelect red淀粉样变性病New FormatterSelect lower case116New Formatter gray line=same database hit hsps color-coded independently淀粉样变性病New Formatter gray line=same117BLAST Output:Alignments&Filterlow complexity sequence filteredlow complexity sequence filtered淀粉样变性病BLAST Output:Alignments&Fil118Advanced OptionsLimit to Organismprotein allfilter Nprotein allfilter NExample Entrez Queriesproteins allFilter NOT mammaliaOrganismray finned fishesOrganismsrcdb refseqProperties Nucleotide only:biomol mrnaPropertiesbiomol genomicPropertiesOtherAdvancede 10000expect value-v 2000descriptions-b 2000alignments-e 10000-v 2000-e 10000-v 2000淀粉样变性病Advanced OptionsLimit to Organ119Genome BLAST Examples淀粉样变性病Genome BLAST Examples淀粉样变性病120Example Search Pathways:HemochromatosisGeneOMIMOMIMGeneGene“hemochromatosis”nucleotide sequenceGenomeBLASTMap ViewerSNPProteinDomainstext searchsequence search淀粉样变性病Example Search Pathways:Hemoc121Sample淀粉样变性病Sample淀粉样变性病122Example:Human Genome BLAST TGCCTCCTTTGGTGAAGGTGACACATCATGTGACCTCTTCAGTGACCACTCTACGGTGTCGGGCCTTGAACTACTACCCCCAGAACATCACCATGAAGTGGCTGAAGGATAAGCAGCCAATGGATGCCAAGGAGTTCGAACCTAAAGACGTATTGCC