Below are the solutions to these exercises on Manipulate Biological Data Using Biostrings Package.
#################### # # # Exercise 1 # # # #################### library(Biostrings) RNA1 <-RNAString("AAGAAAACCAUGAUGGAAGCCAG") palindrome<-findPalindromes(RNA1) print(palindrome)
## Views on a 23-letter RNAString subject ## subject: AAGAAAACCAUGAUGGAAGCCAG ## views: ## start end width ## [1] 8 16 9 [CCAUGAUGG]
#################### # # # Exercise 2 # # # #################### library(Biostrings) DNA1 <- DNAString("AAGAAAACCATGATGGAAGCCAG") palindrome<-findPalindromes(DNA1) print(palindrome)
## Views on a 23-letter DNAString subject ## subject: AAGAAAACCATGATGGAAGCCAG ## views: ## start end width ## [1] 8 16 9 [CCATGATGG]
#################### # # # Exercise 3 # # # #################### library(Biostrings) DNA1 <- DNAString("AAGAAAACCATGATGGAAGCCAG") print(dinucleotideFrequency(DNA1))
## AA AC AG AT CA CC CG CT GA GC GG GT TA TC TG TT ## 5 1 3 2 2 2 0 0 3 1 1 0 0 0 2 0
#################### # # # Exercise 4 # # # #################### library(Biostrings) RNA1 <-RNAString("AUAGUAGAUGCGGCGCGCUAGAG") print(dinucleotideFrequency(RNA1))
## AA AC AG AU CA CC CG CU GA GC GG GU UA UC UG UU ## 0 0 4 2 0 0 3 1 2 4 1 1 3 0 1 0
#################### # # # Exercise 5 # # # #################### library(Biostrings) DNA1 <- DNAString("AAGAAAACCATGATGGAAGCCAG") print(oligonucleotideFrequency(DNA1,4))
## AAAA AAAC AAAG AAAT AACA AACC AACG AACT AAGA AAGC AAGG AAGT AATA AATC AATG ## 1 1 0 0 0 1 0 0 1 1 0 0 0 0 0 ## AATT ACAA ACAC ACAG ACAT ACCA ACCC ACCG ACCT ACGA ACGC ACGG ACGT ACTA ACTC ## 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 ## ACTG ACTT AGAA AGAC AGAG AGAT AGCA AGCC AGCG AGCT AGGA AGGC AGGG AGGT AGTA ## 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 ## AGTC AGTG AGTT ATAA ATAC ATAG ATAT ATCA ATCC ATCG ATCT ATGA ATGC ATGG ATGT ## 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 ## ATTA ATTC ATTG ATTT CAAA CAAC CAAG CAAT CACA CACC CACG CACT CAGA CAGC CAGG ## 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ## CAGT CATA CATC CATG CATT CCAA CCAC CCAG CCAT CCCA CCCC CCCG CCCT CCGA CCGC ## 0 0 0 1 0 0 0 1 1 0 0 0 0 0 0 ## CCGG CCGT CCTA CCTC CCTG CCTT CGAA CGAC CGAG CGAT CGCA CGCC CGCG CGCT CGGA ## 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ## CGGC CGGG CGGT CGTA CGTC CGTG CGTT CTAA CTAC CTAG CTAT CTCA CTCC CTCG CTCT ## 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ## CTGA CTGC CTGG CTGT CTTA CTTC CTTG CTTT GAAA GAAC GAAG GAAT GACA GACC GACG ## 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 ## GACT GAGA GAGC GAGG GAGT GATA GATC GATG GATT GCAA GCAC GCAG GCAT GCCA GCCC ## 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 ## GCCG GCCT GCGA GCGC GCGG GCGT GCTA GCTC GCTG GCTT GGAA GGAC GGAG GGAT GGCA ## 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 ## GGCC GGCG GGCT GGGA GGGC GGGG GGGT GGTA GGTC GGTG GGTT GTAA GTAC GTAG GTAT ## 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ## GTCA GTCC GTCG GTCT GTGA GTGC GTGG GTGT GTTA GTTC GTTG GTTT TAAA TAAC TAAG ## 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ## TAAT TACA TACC TACG TACT TAGA TAGC TAGG TAGT TATA TATC TATG TATT TCAA TCAC ## 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ## TCAG TCAT TCCA TCCC TCCG TCCT TCGA TCGC TCGG TCGT TCTA TCTC TCTG TCTT TGAA ## 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ## TGAC TGAG TGAT TGCA TGCC TGCG TGCT TGGA TGGC TGGG TGGT TGTA TGTC TGTG TGTT ## 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 ## TTAA TTAC TTAG TTAT TTCA TTCC TTCG TTCT TTGA TTGC TTGG TTGT TTTA TTTC TTTG ## 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ## TTTT ## 0
#################### # # # Exercise 6 # # # #################### library(Biostrings) RNA1 <-RNAString("AUAGUAGAUGCGGCGCGCUAGAG") print(oligonucleotideFrequency(RNA1,4))
## AAAA AAAC AAAG AAAU AACA AACC AACG AACU AAGA AAGC AAGG AAGU AAUA AAUC AAUG ## 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ## AAUU ACAA ACAC ACAG ACAU ACCA ACCC ACCG ACCU ACGA ACGC ACGG ACGU ACUA ACUC ## 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ## ACUG ACUU AGAA AGAC AGAG AGAU AGCA AGCC AGCG AGCU AGGA AGGC AGGG AGGU AGUA ## 0 0 0 0 1 1 0 0 0 0 0 0 0 0 1 ## AGUC AGUG AGUU AUAA AUAC AUAG AUAU AUCA AUCC AUCG AUCU AUGA AUGC AUGG AUGU ## 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 ## AUUA AUUC AUUG AUUU CAAA CAAC CAAG CAAU CACA CACC CACG CACU CAGA CAGC CAGG ## 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ## CAGU CAUA CAUC CAUG CAUU CCAA CCAC CCAG CCAU CCCA CCCC CCCG CCCU CCGA CCGC ## 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ## CCGG CCGU CCUA CCUC CCUG CCUU CGAA CGAC CGAG CGAU CGCA CGCC CGCG CGCU CGGA ## 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 ## CGGC CGGG CGGU CGUA CGUC CGUG CGUU CUAA CUAC CUAG CUAU CUCA CUCC CUCG CUCU ## 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 ## CUGA CUGC CUGG CUGU CUUA CUUC CUUG CUUU GAAA GAAC GAAG GAAU GACA GACC GACG ## 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ## GACU GAGA GAGC GAGG GAGU GAUA GAUC GAUG GAUU GCAA GCAC GCAG GCAU GCCA GCCC ## 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 ## GCCG GCCU GCGA GCGC GCGG GCGU GCUA GCUC GCUG GCUU GGAA GGAC GGAG GGAU GGCA ## 0 0 0 2 1 0 1 0 0 0 0 0 0 0 0 ## GGCC GGCG GGCU GGGA GGGC GGGG GGGU GGUA GGUC GGUG GGUU GUAA GUAC GUAG GUAU ## 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 ## GUCA GUCC GUCG GUCU GUGA GUGC GUGG GUGU GUUA GUUC GUUG GUUU UAAA UAAC UAAG ## 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ## UAAU UACA UACC UACG UACU UAGA UAGC UAGG UAGU UAUA UAUC UAUG UAUU UCAA UCAC ## 0 0 0 0 0 2 0 0 1 0 0 0 0 0 0 ## UCAG UCAU UCCA UCCC UCCG UCCU UCGA UCGC UCGG UCGU UCUA UCUC UCUG UCUU UGAA ## 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ## UGAC UGAG UGAU UGCA UGCC UGCG UGCU UGGA UGGC UGGG UGGU UGUA UGUC UGUG UGUU ## 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 ## UUAA UUAC UUAG UUAU UUCA UUCC UUCG UUCU UUGA UUGC UUGG UUGU UUUA UUUC UUUG ## 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ## UUUU ## 0
#################### # # # Exercise 7 # # # #################### library(Biostrings) DNA1 <- DNAString("AAGAAAACCATGATGGAAGCCAG") print(trinucleotideFrequency(DNA1))
## AAA AAC AAG AAT ACA ACC ACG ACT AGA AGC AGG AGT ATA ATC ATG ATT CAA CAC ## 2 1 2 0 0 1 0 0 1 1 0 0 0 0 2 0 0 0 ## CAG CAT CCA CCC CCG CCT CGA CGC CGG CGT CTA CTC CTG CTT GAA GAC GAG GAT ## 1 1 2 0 0 0 0 0 0 0 0 0 0 0 2 0 0 1 ## GCA GCC GCG GCT GGA GGC GGG GGT GTA GTC GTG GTT TAA TAC TAG TAT TCA TCC ## 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 ## TCG TCT TGA TGC TGG TGT TTA TTC TTG TTT ## 0 0 1 0 1 0 0 0 0 0
#################### # # # Exercise 8 # # # #################### library(Biostrings) RNA1 <-RNAString("AUAGUAGAUGCGGCGCGCUAGAG") print(trinucleotideFrequency(RNA1))
## AAA AAC AAG AAU ACA ACC ACG ACU AGA AGC AGG AGU AUA AUC AUG AUU CAA CAC ## 0 0 0 0 0 0 0 0 2 0 0 1 1 0 1 0 0 0 ## CAG CAU CCA CCC CCG CCU CGA CGC CGG CGU CUA CUC CUG CUU GAA GAC GAG GAU ## 0 0 0 0 0 0 0 2 1 0 1 0 0 0 0 0 1 1 ## GCA GCC GCG GCU GGA GGC GGG GGU GUA GUC GUG GUU UAA UAC UAG UAU UCA UCC ## 0 0 3 1 0 1 0 0 1 0 0 0 0 0 3 0 0 0 ## UCG UCU UGA UGC UGG UGU UUA UUC UUG UUU ## 0 0 0 1 0 0 0 0 0 0
#################### # # # Exercise 9 # # # #################### library(Biostrings) print(alphabet(AAString()))
## [1] "A" "R" "N" "D" "C" "Q" "E" "G" "H" "I" "L" "K" "M" "F" "P" "S" "T" ## [18] "W" "Y" "V" "U" "O" "B" "J" "Z" "X" "*" "-" "+" "."
#################### # # # Exercise 10 # # # #################### library(Biostrings) Amino1 <- AAString("MVVVDFFV") print(length(Amino1))
## [1] 8
print(alphabetFrequency(Amino1))
## A R N D C Q E G H I L K ## 0 0 0 1 0 0 0 0 0 0 0 0 ## M F P S T W Y V U O B J ## 1 2 0 0 0 0 0 4 0 0 0 0 ## Z X * - + . other ## 0 0 0 0 0 0 0
Related exercise sets:
Bioinformatics Tutorial with Exercises in R (part 1)
Manipulate Biological Data Using Biostrings Package Exercises (Part 1)
Manipulate Biological Data Using Biostrings Package Exercises(Part 2)
Repeated measures ANOVA in R Exercises
Manipulate Biological Data Using Biostrings Package Exercises(Part 3)
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