淀粉样变性病

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1、淀粉样变性病淀粉样变性病NCBI FieldGuideGenome ResourcesLocusLinkLocusLinkLocusLinkLocusLinkGene databaseGene databaseGene databaseGene databaseUniGeneUniGeneUniGeneUniGeneTrace ArchiveTrace ArchiveTrace ArchiveTrace ArchiveMap ViewerMap ViewerMap ViewerMap ViewerHomologeneHomologeneHomologeneHomologeneNCBI Fiel

2、dGuideGenomic BiologyNCBI FieldGuideNCBI FieldGuideNCBI FieldGuideNCBI FieldGuideGenome Projects: microbNCBI FieldGuideNCBI FieldGuideNCBI FieldGuideGenome ResourcesLocusLinkLocusLinkLocusLinkLocusLinkGene databaseGene databaseGene databaseGene databaseUniGeneUniGeneUniGeneUniGeneTrace ArchiveTrace

3、ArchiveTrace ArchiveTrace ArchiveMap ViewerMap ViewerMap ViewerMap ViewerHomologeneHomologeneHomologeneHomologeneNCBI FieldGuideA single query interface to SequencesSequences- RefSeqs- RefSeqs- GenBank- GenBank- - HomologeneHomologeneMaps Maps MapViewerMapViewerEntrez linksEntrez linksLocusLinkLocus

4、Link 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 MapViewerMapViewerEntrez linksEntrez linksEntrez G

5、ene 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/Introns: Gene TableNCBI FieldGui

6、deGene 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血色沉着病NCBI FieldGuideLinking t

7、o 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 ArchiveMap ViewerMap ViewerMa

8、p 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 locations Useful for gene discov

9、ery 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 FieldGuideUniGene Cluster Hs.95351

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

11、aseUniGeneUniGeneUniGeneUniGeneTrace ArchiveTrace ArchiveTrace ArchiveTrace ArchiveMap ViewerMap ViewerMap ViewerMap ViewerHomologeneHomologeneHomologeneHomologeneNCBI FieldGuideThe New HomologeneAutomated detection of homologs among the annotated genes of completely sequenced eukaryotic genomes. No

12、 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。请参考文献获得更多的信息。NCBI FieldGuideg

13、ene 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 Homologenerag112recombination ac

14、tivating gene NCBI FieldGuideRAG1 HomolgeneRAG1Amniota NCBI FieldGuideHomolgene: RAG1NCBI FieldGuideNCBI FieldGuideHomolgene: RAG1NCBI FieldGuideGenome ResourcesLocusLinkLocusLinkLocusLinkLocusLinkGene databaseGene databaseGene databaseGene databaseUniGeneUniGeneUniGeneUniGeneTrace ArchiveTrace Arch

15、iveTrace ArchiveTrace ArchiveMap ViewerMap ViewerMap ViewerMap ViewerHomologeneHomologeneHomologeneHomologeneNCBI FieldGuideNCBI FieldGuideNCBI FieldGuideNCBI FieldGuideMapViewerNCBI FieldGuideList ViewNCBI FieldGuideHuman MapVieweradar腺甙脱氨酶NCBI FieldGuideMapViewer: Human ADAR4NCBI FieldGuideMV Hs A

16、DAR3 UTR5 UTRNCBI FieldGuideMaps & Options-Sequence mapsSequence maps-Ab initioAssemblyRepeatsBES_CloneCloneNCI_CloneContigComponentCpG islanddbSNP haplotypeFosmidGenBank_DNAGenePhenotypeSAGE_TagSTSTCAG_RNATranscript (RNA)Hs_UniGeneHs_EST-Cytogenetic mapsCytogenetic maps-IdeogramFISH CloneGene_Cytog

17、eneticMitelman 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 FieldGuideMapViewerUniGen

18、eComponentRepeatsGeneNCBI FieldGuideMaster map: repeatsNCBI FieldGuideGenePhenotypeVariationNCBI FieldGuideMaps & OptionsMaps & OptionsNCBI FieldGuideGenome ResourcesLocusLinkLocusLinkLocusLinkLocusLinkGene databaseGene databaseGene databaseGene databaseUniGeneUniGeneUniGeneUniGeneTrace ArchiveTrace

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

20、StructureNCBI 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 relationshipsOther:model

21、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: HEWASHEREBUTNOWISHERE

22、(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 an

23、d 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 searchesNCBI FieldGuideWide

24、ly 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 tbla

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

26、thoutprotein annotations, 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 WordsGTAC

27、TGGACATGGACCCTACAGGAAQuery:GTACTGGACAT TACTGGACATG ACTGGACATGG CTGGACATGGA TGGACATGGAC GGACATGGACC GACATGGACCC ACATGGACCCTMake a lookuptable of words11-mer. . .828megablast711blastnminimumdefaultWORD SIZENCBI FieldGuideProtein WordsGTQITVEDLFYNIATRRKALKNQuery: Neighborhood WordsLTV, MTV, ISV, LSV, e

28、tc.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 NCBI FieldGuideMinimum Requirements for a Hit Nucleotide BLAST requires one exact match Protein BLAST requires two neighboring matches within 40 aaGTQITVEDLFYNI S

29、EI YYNATCGCCATGCTTAATTGGGCTT CATGCTTAATT neighborhood wordsone exact matchtwo matches -A 40 = blastp default NCBI FieldGuideBLASTP Summary YLS HFLSbjct 287 LEETYAKYLHKGASYFVYLSLNMSPEQLDVNVHPSKRIVHFLYDQEI 333 Query 1 IETVYAAYLPKNTHPFLYLSLEISPQNVDVNVHPTKHEVHFLHEESI 47Gapped extension with trace backGa

30、pped 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

31、(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 wordsNCBI FieldGu

32、ideScoring 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 NCBI FieldGuideScoring Systems - ProteinsPosition Independent MatricesPAM Matrices (Percent Accepted Mutation) Derived

33、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 iden

34、tity cutoff BLOSUM62 - default matrix for BLASTPosition Specific Score Matrices (PSSMs)PSI- and 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

35、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

36、-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 substitutionsN

37、CBI 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 -1 -1 437 S 0 0 -1 0 1 1

38、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 -

39、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

40、 -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

41、 -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 -

42、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 between two random s

43、equencesfollow 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 scoreexpect

44、ed number of random hitsMore info: www.ncbi.nlm.nih.gov/BLAST/tutorial/Altschul-1.html NCBI FieldGuideAdvanced BLAST Options: NucleotideExample Entrez Queriesnucleotide allFilter NOT mammaliaOrganismgreen plantsOrganismbiomol mrnaPropertiesgbdiv estProperties AND ratorganismOther Advancede 10000 exp

45、ect value-v 2000 descriptions-b 2000 alignmentsNCBI FieldGuideAdvanced BLAST Options: ProteinMatrix SelectionPAM30 - most stringentBLOSUM45 - least stringentExample Entrez Queriesproteins allFilter NOT mammaliaOrganismgreen plantsOrganismsrcdb refseqPropertiesOther Advancede 10000 expect value-v 200

46、0 descriptions-b 2000 alignmentsLimit by taxonMus musculusOrganismMammaliaOrganismViridiplantaeOrganismNCBI 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%), Gap

47、s = 4/131 (3%)Query: 362 STTSLTSSSTSGSSDKVYAHQMVRTDSREQKLDAFLQPLSKPLS-SQPQAIVTEDKTD 418 S+S SSS+S SS + + +S + + S S S+ + E K Sbjct: 29 SSSSSESSSSSSSSSESESESESESESSSSSSSSDSESSSSSSSDSESEAETKKEESKDS 88FilteredUnfilteredLow Complexity FilteringNCBI FieldGuideOther BLAST Algorithms MegablastDiscontiguous

48、 MegablastPSI-BLASTPHI-BLASTNCBI FieldGuideMegablast: NCBIs Genome Annotator Long alignments of similar DNA sequencesGreedy algorithmConcatenation of query sequencesFaster than blastn; less sensitiveNCBI FieldGuideMegaBLAST & Word SizeTrade-off: sensitivity vs speed23blastp828megablast711blastnminim

49、umdefaultWORD SIZENCBI FieldGuideDiscontiguous MegablastUses discontiguous word matchesBetter for cross-species comparisonsNCBI FieldGuideTemplates for Discontiguous WordsW = 11, t = 16, coding: 1101101101101101W = 11, t = 16, non-coding: 1110010110110111W = 12, t = 16, coding: 1111101101101101W = 1

50、2, 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: 111010010100

51、010010111W = 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 lengthNCBI Fie

52、ldGuideDiscontiguous (Cross-species) MegaBLASTNCBI FieldGuideDiscontiguous Word OptionsNCBI FieldGuideMegaBLAST vs Discontiguous MegaBLASTNM_017460Homo sapiens cytochrome P450, family 3, subfamily A, polypeptide 4 (CYP3A4), transcript variant 1, mRNA (2768 letters) vs DrosophilaNCBI FieldGuideMegaBL

53、AST vs Discontiguous MegaBLAST MegaBLAST = “No significant similarity found.” Discontiguous megaBLAST =NCBI FieldGuideAnother Example . . . Discontiguous megaBLAST = numerous hits . . .Query: NM_078651 Drosophila melanogaster CG18582-PA (mbt) mRNA, (3244 bp)/note= mushroom bodies tiny; synonyms: Pak

54、2, STE20, dPAK2 MegaBLAST = “No significant similarity found.”Database: nr (nt), MammaliaorgnNCBI FieldGuideEx: Discontiguous MegaBLASTNCBI FieldGuideEx: BLASTNNCBI FieldGuidePSI-BLASTExample: Confirming relationships of purinenucleotide metabolism proteinsPosition-specific Iterated BLASTNCBI FieldG

55、uidegi|113340|sp|P03958|ADA_MOUSE ADENOSINE DEAMINASE (ADENOSINEMAQTPAFNKPKVELHVHLDGAIKPETILYFGKKRGIALPADTVEELRNIIGMDKPLSLPGFVIAGCREAIKRIAYEFVEMKAKEGVVYVEVRYSPHLLANSKVDPMPWNQTEGDVTPDDVVDEQAFGIKVRSILCCMRHQPSWSLEVLELCKKYNQKTVVAMDLAGDETIEGSSLFPGHVEAYRTVHAGEVGSPEVVREAVDILKTERVGHGYHTIEDEALYNRLLKENMHFEVCP

56、WSSYLTGAVRFKNDKANYSLNTDDPLIFKSTLDTDYQMTKKDMGFTEEEFKRLNINAAKSSFLPEEEKKPSI-BLAST0.005E value cutoff for PSSMNCBI FieldGuideRESULTS: Initial BLASTPSame results as protein-protein BLAST; different formatNCBI FieldGuideResults of First PSSM SearchOther purine nucleotide metabolizing enzymes not found by

57、ordinary BLASTNCBI FieldGuideTenth PSSM Search: ConvergenceJust below threshold, another nucleotide metabolism enzymeCheck to add to PSSMNCBI FieldGuideReverse PSI-BLAST (RPS)-BLASTNCBI FieldGuideAdenosine/AMP Deaminase DomainAMP Deaminases. . . .NCBI FieldGuidePHI-BLASTgi|231729|sp|P30429|CED4_CAEE

58、L CELL DEATH PROTEIN 4MLCEIECRALSTAHTRLIHDFEPRDALTYLEGKNIFTEDHSELISKMSTRLERIANFLRIYRRQASELIDFFNYNNQSHLADFLEDYIDFAINEPDLLRPVVIAPQFSRQMLDRKLLLGNVPKQMTCYIREYHVIKKLDEMCDLDSFFLFLHGRAGSGKSVIASQALSKSDQLIGINYDSIVWLKDSGTAPKSTFDLFTDILKSEDDLLNFPSVEHVTSVVLKRMICNALIDRPNTLFVFDDVVQEETIRWAQELRLRCLVTTRDVEIASQTCEFIEV

59、TSLEIDECYDFLEAYGMPMPVGEKEEDVLNKTIELSSGNPATLMMFFKSCEPKTFEKGAxxxxGKSTNCBI FieldGuideWhats Whats New?New?NCBI FieldGuideBLAST DatabasesNucleotiderefseq_rna = NM_*, XM_*refseq_genomic = NC_*, NG_*env_ntenvironmental samplefilter, e.g., 16S rRNAProteinrefseq = NP_*, XP_*env_nrNCBI FieldGuideNew Formatter

60、Select lower caseSelect redNCBI FieldGuideNew Formatter gray line = same database hit hsps color-coded independentlyNCBI FieldGuideBLAST Output: Alignments & Filterlow complexity sequence filteredlow complexity sequence filteredNCBI FieldGuideAdvanced OptionsLimit to Organismprotein allfilter Nprote

61、in 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 2000NCBI FieldGuideG

62、enome BLAST ExamplesNCBI FieldGuideExample Search Pathways: HemochromatosisGeneOMIMOMIMGeneGene“hemochromatosis”nucleotide sequenceGenomeBLASTMap ViewerSNPProteinDomainstext searchsequence searchNCBI FieldGuideSampleNCBI FieldGuideExample: Human Genome BLAST TGCCTCCTTTGGTGAAGGTGACACATCATGTGACCTCTTCA

63、GTGACCACTCTACGGTGTCGGGCCTTGAACTACTACCCCCAGAACATCACCATGAAGTGGCTGAAGGATAAGCAGCCAATGGATGCCAAGGAGTTCGAACCTAAAGACGTATTGCCCAATGGGGATGGGACCTACCAGGGCTGGATAACCTTGGCTGTACCCCCTGGGGAAGAGCHuman ESTNCBI FieldGuideHuman Genome BLAST: Results NCBI FieldGuideHuman Genome BLAST: MapViewerEntrez GeneEntrez GeneEntrez

64、GeneEntrez GeneNCBI FieldGuideMap Oligos Onto GenomeCCATGGCGACCCTGGAAAAGCNNNNNNNNNNCAGCAGCGGCTGTGCCTGCGG-W 7 e 1000forward primerreverse primerNCBI FieldGuideGenome BLAST ResultsNCBI FieldGuidePrimer Alignmentsforward primerreverse primerNCBI FieldGuideMapViewerNCBI FieldGuideMapViewerNCBI FieldGuid

65、eSequence View (sv)forwardreverseNCBI FieldGuideftp:/ftp.ncbi.nih.gov/refseq/LocusLink/LL_tmpl.gzA Few Good Filesftp:/ftp.ncbi.nih.gov/refseq/release/genomic.fna.gzftp:/ftp.ncbi.nih.gov/repository/UniGene/Hs.seq.uniq.gzftp:/ftp.ncbi.nih.gov/pub/mmdb/cdd/ftp:/ftp.ncbi.nih.gov/toolbox/ncbi_tools/ncbi.tar.gzftp:/ftp.ncbi.nlm.nih.gov/gene/DATA/gene_info.gzNCBI FieldGuideService AddressesBLASTBLASTblast-helpncbi.nlm.nih.govGeneral HelpGeneral Helpinfoncbi.nlm.nih.govWayne Wayne MattenMatten mattenncbi.nlm.nih.gov