1、NCBI FieldGuideA Field Guide part 2 Genome resources Sequence similarityApr, 2007Shandong UniversityNCBI FieldGuideGenome ResourcesNCBI FieldGuideGenomic BiologyNCBI FieldGuideNCBI FieldGuideNCBI FieldGuideNCBI FieldGuideGenome Projects: microbNCBI FieldGuideNCBI FieldGuideNCBI FieldGuideGenome Reso
2、urcesNCBI FieldGuideA single query interface to SequencesSequences- RefSeqs- RefSeqs- GenBank- GenBank- - HomologeneHomologeneMaps Maps MapViewerMapViewerEntrez linksEntrez linksLocusLinkLocusLink will be replaced by Entrez Gene on MARCH 1, 2005. Check Gene FAQ for current information.NCBI FieldGuid
3、eEntrez GeneLocusLinkA single query interface to SequencesSequences - RefSeqs - RefSeqs - GenBank - GenBank - - HomologeneHomologeneMaps Maps MapViewerMapViewerEntrez linksEntrez linksEntrez Gene More organisms - all RefSeq genomes Entrez integrationNCBI FieldGuideGsnsym淀粉样变性病NCBI FieldGuideNCBI Fie
4、ldGuideGlobal Entrez: NADH2nadh247NCBI FieldGuideEntrez Gene: NADH226 recordsNCBI FieldGuideGene Record for Pongo NADH2Homo sapiensNCBI FieldGuideDisplay Exons/Introns: Gene TableNCBI FieldGuideGene TableNCBI FieldGuideA Record With More Data: Human HFE血色沉着病NCBI FieldGuideGene Graphic LinksNM_NM_NP_
5、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 to SNP染色体定位基因定位序列定位NCBI FieldGuideSNP in StructureNCBI FieldGuideLink to OMIMNCBI FieldGuideVariants in OMIMN
6、CBI FieldGuideGenome ResourcesNCBI 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 discovery and selection of mapping reagentsUniGe
7、neNCBI 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.95351NCBI FieldGuideUniGene Cluster Hs.95351NCB
8、I FieldGuideUniGene Cluster Hs.95351: expressionNCBI FieldGuideUniGene Cluster Hs.95351: seqsNCBI FieldGuideDownload sequencesweb pageftp siteNCBI FieldGuideGenome ResourcesNCBI FieldGuideThe New HomologeneAutomated detection of homologs among the annotated genes of completely sequenced eukaryotic g
9、enomes. No longer UniGene based Protein similarities first Guided by taxonomic tree Includes 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。NCB
10、I 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 Homologenerag112rec
11、ombination activating gene NCBI FieldGuideRAG1 HomolgeneRAG1Amniota NCBI FieldGuideHomolgene: RAG1NCBI FieldGuideNCBI FieldGuideHomolgene: RAG1NCBI FieldGuideGenome ResourcesNCBI FieldGuideNCBI FieldGuideNCBI FieldGuideNCBI FieldGuideMapViewerNCBI FieldGuideList ViewNCBI FieldGuideHuman MapViewerada
12、r腺甙脱氨酶NCBI FieldGuideMapViewer: Human ADAR4NCBI FieldGuideMV Hs ADAR3 UTR5 UTRNCBI FieldGuideMaps & Options-Sequence mapsSequence maps-Ab initioAssemblyRepeatsBES_CloneCloneNCI_CloneContigComponentCpG islanddbSNP haplotypeFosmidGenBank_DNAGenePhenotypeSAGE_TagSTSTCAG_RNATranscript (RNA)Hs_UniGeneHs_
13、EST-CytogeneticCytogenetic maps 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_UniGene
14、Gga_ESTVariationMaps & Options= SNPNCBI FieldGuideMapViewerUniGeneComponentRepeatsGeneNCBI FieldGuideMaster map: repeatsNCBI FieldGuideGenePhenotypeVariationNCBI FieldGuideMaps & OptionsMaps & OptionsNCBI FieldGuideGenome ResourcesNCBI FieldGuideNCBI FieldGuideNCBI FieldGuideStrongylocentrotus purpu
15、ratus TracesNCBI FieldGuideBasic Local Alignment Search ToolNCBI FieldGuideWeb AccessBLASTVASTEntrezTextSequenceStructureNCBI FieldGuideNCBI FieldGuideBasic Local Alignment Search Tool Why use sequence similarity? BLAST algorithm BLAST statistics BLAST output ExamplesNCBI FieldGuideWhy Do We Need Se
16、quence Similarity Searching? To identify and annotate sequences To evaluate evolutionary relationships Other: model genomic structure (e.g., Spidey) check primer specificity in silico: NCBIs toolNCBI FieldGuideBLAST Website StatsNCBI FieldGuideGlobal vs Local AlignmentSeq 1Seq 2Seq 1Seq 2Global alig
17、nmentLocal alignmentNCBI FieldGuideGlobal 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 21NCBI FieldGuideT
18、he Flavors of BLAST Standard BLAST traditional “contiguous” word hit position independent scoring nucleotide, protein and translations (blastn, blastp, blastx, tblastn, tblastx) Megablast optimized for large batch searches can use discontiguous words PSI-BLAST constructs PSSMs automatically; uses as
19、 query very sensitive protein search RPS BLAST searches a database of PSSMs tool for conserved domain searchesNCBI FieldGuide Widely used similarity search tool Heuristic approach based on Smith Waterman algorithm Finds best local alignments Provides statistical significance All combinations (DNA/Pr
20、otein) query and database. . DNA vs DNA blastn DNA translation vs Protein blastx Protein vs Protein blastp Protein vs DNA translation tblastn DNA translation vs DNA translation tblastx www, standalone, and network clientsBasic Local Alignment Search ToolNCBI FieldGuideTranslated BLASTQueryQueryDatab
21、aseDatabaseProgramProgramNPucleotideroteinNNNNPPblastxtblastntblastxPPPPPPPPPPPPPPPPPPPPPPPPParticularly useful for nucleotide sequences withoutprotein annotations, such as ESTs or genomic DNANCBI FieldGuideHow BLAST Works Make lookup table of “words” for query Scan database for hits Ungapped extens
22、ions of hits (initial HSPs) Gapped extensions (no traceback) Gapped extensions (traceback; alignment details)NCBI FieldGuideNucleotide WordsGTACTGGACATGGACCCTACAGGAAQuery:GTACTGGACAT TACTGGACATG ACTGGACATGG CTGGACATGGA TGGACATGGAC GGACATGGACC GACATGGACCC ACATGGACCCTMake a lookuptable of words11-mer.
23、 . .828megablast711blastnminimumdefaultWORD SIZENCBI FieldGuideProtein 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 NCBI FieldGuideMin
24、imum 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 NCBI FieldGuideBLASTP Summary YLS HFLSbjct 287
25、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 LEETYAKYL
26、HKGASYFVYLSLNMSPEQLDVNVHPSKRIVHFLYDQEIATSI 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 thresho
27、ldscore 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 +1 -3T 3 3 3 +1Identity matrixCAGGTAGCAAGCTTGCATGTCA| | | raw score = 19-9 = 10CACGTAGCA
28、AGCTTG-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 calculated from PAM1 PAM250 widely usedBLOSUM Matrices (BLOck SUbstitution Mat
29、rices) 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-BLASTNCBI FieldGuideA 4R -1 5 N -2 0 6D -2 -2 1 6C 0 -3
30、-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
31、 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
32、 -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 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
33、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 -
34、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
35、 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
36、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
37、-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 ./bl
38、astpgp -i NP_499868.2 -d nr -j 3 -Q NP_499868.pssm NCBI FieldGuideLocal 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 fo
39、r 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: www.ncbi.nlm.nih.gov/BLAST/tutorial/Altschul-1.html NCBI FieldGuideAdvanced BLAST Options: NucleotideExample Entrez Queri
40、esnucleotide allFilter NOT mammaliaOrganismgreen plantsOrganismbiomol mrnaPropertiesgbdiv estProperties AND ratorganismOther Advancede 10000 expect value-v 2000 descriptions-b 2000 alignmentsNCBI FieldGuideAdvanced BLAST Options: ProteinMatrix SelectionPAM30 - most stringentBLOSUM45 - least stringen
41、tExample Entrez Queriesproteins allFilter NOT mammaliaOrganismgreen plantsOrganismsrcdb refseqPropertiesOther Advancede 10000 expect value-v 2000 descriptions-b 2000 alignmentsLimit by taxonMus musculusOrganismMammaliaOrganismViridiplantaeOrganismNCBI FieldGuide sp|P27476|NSR1_YEAST NUCLEAR LOCALIZA
42、TION 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 SSSSSESSSSSSSSSESESES
43、ESESESSSSSSSSDSESSSSSSSDSESEAETKKEESKDS 88FilteredUnfilteredLow Complexity FilteringNCBI FieldGuideOther BLAST Algorithms Megablast Discontiguous Megablast PSI-BLAST PHI-BLASTNCBI FieldGuideMegablast: NCBIs Genome Annotator Long alignments of similar DNA sequences Greedy algorithm Concatenation of q
44、uery sequences Faster than blastn; less sensitiveNCBI FieldGuideMegaBLAST & Word SizeTrade-off: sensitivity vs speed23blastp828megablast711blastnminimumdefaultWORD SIZENCBI FieldGuideDiscontiguous Megablast Uses discontiguous word matches Better for cross-species comparisonsNCBI FieldGuideTemplates
45、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, codin
46、g: 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. PatternHu
47、nter: faster and more sensitive homology 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_017460H
48、omo sapiens cytochrome P450, family 3, subfamily A, polypeptide 4 (CYP3A4), transcript variant 1, mRNA (2768 letters) vs DrosophilaNCBI FieldGuideMegaBLAST vs Discontiguous MegaBLAST MegaBLAST = “No significant similarity found.” Discontiguous megaBLAST =NCBI FieldGuideAnother Example . . . Disconti
49、guous 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), MammaliaorgnNCBI FieldGuideEx: Discontiguous MegaBLASTNCBI FieldGui
50、deEx: BLASTNNCBI FieldGuidePSI-BLASTExample: Confirming relationships of purinenucleotide metabolism proteinsPosition-specific Iterated BLASTNCBI FieldGuidegi|113340|sp|P03958|ADA_MOUSE ADENOSINE DEAMINASE (ADENOSINEMAQTPAFNKPKVELHVHLDGAIKPETILYFGKKRGIALPADTVEELRNIIGMDKPLSLPGFVIAGCREAIKRIAYEFVEMKAKE
