Skoringmatriks.docx

library(Biostrings) > skoringmatriks<-nucleotideSubstitutionMatrix(match=2, mismatch=-1, baseonly=TRUE) Error in nucleotideSubstitutionMatrix(match = 2, mismatch = -1, baseonly = TRUE) : unused argument (baseonly = TRUE) > skoringmatriks<-nucleotideSubstitutionMatrix(match=2, mismatch=-1, baseonly=TRUE) Error in nucleotideSubstitutionMatrix(match = 2, mismatch = -1, baseonly = TRUE) : unused argument (baseonly = TRUE) > skoringmatriks<-nucleotideSubstitutionMatrix(match=2, mismatch=-1, baseOnly = =TRUE) Error: unexpected '=' in "skoringmatriks<-nucleotideSubstitutionMatrix(match=2, mismatc h=-1, baseOnly = =" > skoringmatriks<-nucleotideSubstitutionMatrix(match=2, mismatch=-1, baseOnly =TRUE) > skoringmatriks A C G T A 2 -1 -1 -1 C -1 2 -1 -1 G -1 -1 2 -1 T -1 -1 -1 2 > sekuens1<-"ACGTGACTCCTA" > sekuens2<-"GTCAGTAATCG" > penyejajaranglobal<-pairwiseAligment(sekuens1,sekuens2,substitutionMatrix=skoringmatr iks,gapopening=-2,gapExtention=-8,scoreonly=FALSE) Error: could not find function "pairwiseAligment" > penyejajaranglobal<-pairwiseAlignment(sekuens1,sekuens2,substitutionMatrix=skoringmat riks,gapopening=-2,gapExtention=-8,scoreonly=FALSE) Error in .local(pattern, subject, ...) : unused arguments (gapopening = -2, gapExtention = -8, scoreonly = FALSE) > penyejajaranglobal<-pairwiseAlignment(sekuens1,sekuens2,substitutionMatrix=skoringmat riks,gapOpening=-2,gapExtention=-8,scoreOnly=FALSE) Error in .local(pattern, subject, ...) : unused argument (gapExtention = -8) > penyejajaranglobal<-pairwiseAlignment(sekuens1,sekuens2,substitutionMatrix=skoringmat riks,gapOpening=-2,gapExtension=-8,scoreOnly=FALSE) > penyejajaranglobal Global PairwiseAlignmentsSingleSubject (1 of 1) pattern: [1] ACGTGACTCCT subject: [1] GTCAGTAATCG score: -15

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