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exercises_dna-seq-statistics-p1.md

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Exercises - DNA Sequence Statistics

Answers: Rhiannon Cameron

Reference: A Little Book of R for Bioinformatics

Answers assume having run the following: library("seqinr")

Q1 - What are the last twenty nucleotides of the DEN-1 Dengue virus genome sequence?

> dengue <- read.fasta(file="den1.fasta")
> dengueseq <- dengue[[1]]
> length(dengueseq)
[1] 10735
> dengueseq[10716:10735]
[1] "c" "t" "g" "t" "t" "g" "a" "a" "t" "c" "a" "a" "c" "a" "g"
[16] "g" "t" "t" "c" "t"

Q2 - What is the length in nucleotides of the genome sequence for the bacterium Mycobacterium leprae strain TN (accession NC_002677)?

> lepraeTN <- getncbiseq("NC_002677")
Error in acnucopen(bank, socket) : Database with name -->bacterial<-- is currently off for maintenance, please try again later.

Bacterial database appears to be inaccessible by this call, at this time, as it still works to obtain DEN-1 sequence data.

# manually obtained fasta file and imported data.
> lepraeTN <- read.fasta(file="NC_002677-1.fasta")
> lepraeTNseq <- lepraeTN[[1]]

# saved copy, just because.
> write.fasta(names="lepraeTN", sequences=lepraeTNseq, file.out="lepraeTN.fasta")

> length(lepraeTNseq)
[1] 3268203

Q3 - How many of each of the four nucleotides A, C, T and G, and any other symbols, are there in the Mycobacterium leprae TN genome sequence?

> table(lepraeTNseq)
lepraeTNseq
 a      c      g      t 
687041 938713 950202 692247

Q4 - What is the GC content of the Mycobacterium leprae TN genome sequence, when:

(i) ...all non-A/C/T/G nucleotides are included?

> GC(lepraeseq, exact=TRUE)
[1] 0.5779675
# GC Content: 57.79675%

(ii) ...non-A/C/T/G nucleotides are discarded?

> GC(lepraeTNseq) #default: exact=FALSE
[1] 0.5779675
# GC Content: 57.79675%

GC content is the same; therefore, the sequence must not contain any non-A/C/T/G nucleotides.

Q5 - How many of each of the four nucleotides A, C, T and G are there in the complement of the Mycobacterium leprae TN genome sequence?

> lepraeTNseq_comp <- comp(lepraeTNseq)
[1] - [995] # lists nucleotide sequence

> count(lepraeTNseq_comp, 1)
     a      c      g      t 
692247 950202 938713 687041

Q6 - How many occurrences of the DNA words CC, CG and GC occur in the Mycobacterium leprae TN genome sequence?

> count(lepraeTNseq, 2)

aa     ac     ag     at     ca     cc     cg     ct     ga 
149718 206961 170846 159516 224666 236971 306986 170089 203397 
gc     gg     gt     ta     tc     tg     tt 
293261 243071 210473 109259 201520 229299 152169 

> lepraeTNseq_pairs <- count(lepraeTNseq, 2)
> lepraeTNseq_pairs[["cc"]]
[1] 236971
> lepraeTNseq_pairs[["gg"]]
[1] 243071
> lepraeTNseq_pairs[["gc"]]
[1] 293261

Q7 - How many occurrences of the DNA words CC, CG and GC occur in the:

(i) ...first 1000 nucleotides of the Mycobacterium leprae TN genome sequence?

> lepraeTNseq_pairs_1000 <- count(lepraeTNseq[1:1000], 2)
> lepraeTNseq_pairs_1000[["cc"]]
[1] 82
> lepraeTNseq_pairs_1000[["gg"]]
[1] 39
> lepraeTNseq_pairs_1000[["gc"]]
[1] 63

(ii) ...last 1000 nucleotides of the Mycobacterium leprae TN genome sequence?

> length(lepraeTNseq)
[1] 3268203
> 3268203-999
[1] 3267204
> lepraeTNseq_pairs_last <- count(lepraeTNseq[3267204:3268203],2)
> lepraeTNseq_pairs_last[["cc"]]
[1] 81
> lepraeTNseq_pairs_last[["gg"]]
[1] 49
> lepraeTNseq_pairs_last[["gc"]]
[1] 75