文档介绍：SequenceAlignmentBioinformaticsLecture2ChunshengHanMarch9,2011OutlineSequencealignmentdefinedDynamicprogramming,fasta,andblast…ScoringmatrixWhenyouhavegotasequence…SCELTNITIA……>sp|P01228|FSHB_PIGFollitropinbetachainprecursor(Follicle-stimulatinghormonebetasubunit)(FSH-beta)(FSH-B)Length=129Score=275bits(703),Expect=2e-74Identities=120/129(93%),Positives=124/129(96%)Query:SCELTNITIAIEKEECRFCISINTTWCAGYCYTRDLVYKDP60MK+SCELTNITI+EKEECFCISINTTWCAGYCYTRDLVYKDPSbjct:FCISINTTWCAGYCYTRDLVYKDP60Query:61ARPKIQKTCTFKELVYETVRVPGCAHHADSLYTYPVATQCHCGKCDSDSTDCTVRGLGPS120ARPIQKTCTFKELVYETV+VPGCAHHADSLYTYPVAT+CHCGKCDSDSTDCTVRGLGPSSbjct:61ARPNIQKTCTFKELVYETVKVPGCAHHADSLYTYPVATECHCGKCDSDSTDCTVRGLGPS120Query:121YCSFGEMKE129YCSFEMKESbjct:121YCSFSEMKE129Yes,doablastsearch!But,whatdoesallthismean?,(7,21,57)Asequencewithkelementsisak-.{G,A,T,C}forDNA{20aminoacids},monsource.“Natureisatinkererandnotaninventor.”-------GCTAGAGlobalvslocalalignmentGlobalalignment- aaagcggaagtcacag ||.||.||||||.|| aaggctgaagt-atagLocalalignment-: aaagcggaagtcacag ......|||||.... aaggctgaagt-atagSequenceAlignmentswithIndelsEvolutionproducesinsertionsanddeletions(indels)InadditiontosubstitutionsGoodexample:MHHNALQRRTVWVNAYMHHNALQRRTVWVNAYMHHALQRRTVWVNAY-MHH-ALQRRTVWVNAYBlosumScore=2(end=-6)Score=79(gap=-6)AnalignmentmusthaveequallengthalignedsequencesSo,binatoriallydifficultproblemtofindbestindelsolutionGapPenaltiesGapsarepenalisedWritewxtoindicatethepenaltyforagapoflengthxForexample,eachgapscores-6,sowx=-6*monschemeisScore-12foropeningagapAnd-.,wx=-12-2*(x-1)Startandendgappenaltieso