Below are the solutions to these exercises on Manipulate Biological Data Using Biostrings Package.
#################### # # # Exercise 1 # # # #################### library(Biostrings) DNA1 <-DNAString("ATAGTAGATGCGGCGCGCTAGAG") DNA2 <-DNAString("ATGTCGTCGTAGTCGTGTGTCAC") matrix <- nucleotideSubstitutionMatrix(match = 1, mismatch = -3, baseOnly = TRUE) gAlign <-pairwiseAlignment(DNA1, DNA2, substitutionMatrix = matrix, gapOpening = 3, gapExtension = 1) lAlign <-pairwiseAlignment(DNA1, DNA2, type = "local", substitutionMatrix = matrix, gapOpening = 3, gapExtension = 1) oAlign <-pairwiseAlignment(DNA1, DNA2, type = "overlap", substitutionMatrix = matrix, gapOpening = 3, gapExtension = 1) print(lAlign)
## Local PairwiseAlignmentsSingleSubject (1 of 1) ## pattern: [4] GTAG ## subject: [9] GTAG ## score: 4
print(gAlign)
## Global PairwiseAlignmentsSingleSubject (1 of 1) ## pattern: [1] ATAGTAGATGCGGCGCGCTAG---------AG ## subject: [1] AT-GT-----CGTCG---TAGTCGTGTGTCAC ## score: -24
print(oAlign)
## Overlap PairwiseAlignmentsSingleSubject (1 of 1) ## pattern: [1] "" ## subject: [1] "" ## score: 0
#################### # # # Exercise 2 # # # #################### library(Biostrings) DNA1 <-DNAString("ATAGTAGATGCGGCGCGCTAGAG") DNA2 <-DNAString("ATGTCGTCGTAGTCGTGTGTCAC") matrix <- nucleotideSubstitutionMatrix(match = 1, mismatch = -3) gAlign <-pairwiseAlignment(DNA1, DNA2, substitutionMatrix = matrix, gapOpening = 3, gapExtension = 1) print("Written to File, Available in your default R directory")
## [1] "Written to File, Available in your default R directory"
writePairwiseAlignments(gAlign,file="Alignment.aln") #################### # # # Exercise 3 # # # #################### library(Biostrings) Amino1 <- AAString("MALWMRLLPAAAFLALWGPD") Amino2 <- AAString("MALWMRLLPLLALLALWGPD") pAlign<-pairwiseAlignment(Amino1,Amino2) print(pAlign)
## Global PairwiseAlignmentsSingleSubject (1 of 1) ## pattern: [1] MALWMRLLPAAAFLALWGPD ## subject: [1] MALWMRLLPLLALLALWGPD ## score: 54.44525
#################### # # # Exercise 4 # # # #################### library(Biostrings) Amino1 <- AAString("MALWMRLLPAAAFLALWGPD") Amino2 <- AAString("MALWMRLLPLLALLALWGPD") pAlign<-pairwiseAlignment(Amino1,Amino2,substitutionMatrix = "BLOSUM62", gapOpening = 3, gapExtension = 1) print(pAlign)
## Global PairwiseAlignmentsSingleSubject (1 of 1) ## pattern: [1] MALWMRLLPAAAFLALWGPD ## subject: [1] MALWMRLLPLLALLALWGPD ## score: 93
#################### # # # Exercise 5 # # # #################### library(Biostrings) Amino1 <- AAString("MALWMRLLPAAAFLALWGPD") Amino2 <- AAString("MALWMRLLPLLALLALWGPD") pAlign<-pairwiseAlignment(Amino1,Amino2,substitutionMatrix = "BLOSUM100", gapOpening = 3, gapExtension = 1) print(pAlign)
## Global PairwiseAlignmentsSingleSubject (1 of 1) ## pattern: [1] MALWMRLLPAAAFLALWGPD ## subject: [1] MALWMRLLPLLALLALWGPD ## score: 167
#################### # # # Exercise 6 # # # #################### library(Biostrings) Amino1 <- AAString("MALWMRLLPAAAFLALWGPD") Amino2 <- AAString("MALWMRLLPLLALLALWGPD") pAlign<-pairwiseAlignment(Amino1,Amino2,substitutionMatrix = "PAM250", gapOpening = 3, gapExtension = 1) print(pAlign)
## Global PairwiseAlignmentsSingleSubject (1 of 1) ## pattern: [1] MALWMRLLPAAAFLALWGPD ## subject: [1] MALWMRLLPLLALLALWGPD ## score: 107
#################### # # # Exercise 7 # # # #################### library(Biostrings) data(BLOSUM62) rvalues<-BLOSUM62["B", "D"] ncbifile <- "ftp://ftp.ncbi.nih.gov/blast/matrices/BLOSUM62" blosum <- as.matrix(read.table(ncbifile)) ncbivalues<-blosum["B", "D"] print(rvalues)
## [1] 4
print(ncbivalues)
## [1] 4
#################### # # # Exercise 8 # # # #################### options(warn=-1) library(Biostrings) Amino1 <- AAString("MALWMRLLPAAAFLALWGPD") Amino2 <- AAString("MALWMRLLPLLALLALWGPD") align<-needwunsQS(Amino1,Amino2, substmat = "BLOSUM62") print(align)
## Global PairwiseAlignments (1 of 1) ## pattern: [1] MALWMRLLPAAAFLALWGPD ## subject: [1] MALWMRLLPLLALLALWGPD ## score: 93
#################### # # # Exercise 9 # # # #################### library(Biostrings) DNA1 <-DNAString("ATAGTAGATGCGGCGCGCTAGAG") DNA2 <-DNAString("ATGTCGTCGTAGTCGTGTGTCAC") translatedAmino1<-translate(DNA1) translatedAmino2<-translate(DNA2) align<-pairwiseAlignment(translatedAmino1,translatedAmino2) print(align)
## Global PairwiseAlignmentsSingleSubject (1 of 1) ## pattern: [1] IVDAAR* ## subject: [1] MSS*SCV ## score: -43.67328
#################### # # # Exercise 10 # # # #################### library(Biostrings) RNA1 <-RNAString("AUAGUAGAUGCGGCGCGCUAGAG") RNA2 <-RNAString("AUGUCGUCGUAGUCGUGUGUCAC") translatedRNA1<-translate(RNA1) translatedRNA2<-translate(RNA2) align<-pairwiseAlignment(translatedRNA1,translatedRNA2) print(align)
## Global PairwiseAlignmentsSingleSubject (1 of 1) ## pattern: [1] IVDAAR* ## subject: [1] MSS*SCV ## score: -43.67328
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