Lab: DNA exercise

DNA exercise

# vector ... etc.
my_dna <- "AACGAATGAGTAAATGAGTAAATGAAGGAATGATTATTCCTTGCTTTAGAACTTCTGGAATTAGAGGACAATATTAATAATACCATCGCACAGTGTTTCTTTGTTGTTAATGCTACAACATACAAAGAGGAAGCATGCAG"
my_dna

## [1] "AACGAATGAGTAAATGAGTAAATGAAGGAATGATTATTCCTTGCTTTAGAACTTCTGGAATTAGAGGACAATATTAATAATACCATCGCACAGTGTTTCTTTGTTGTTAATGCTACAACATACAAAGAGGAAGCATGCAG"

length(my_dna)

## [1] 1

class(my_dna)

## [1] "character"

str(my_dna)

##  chr "AACGAATGAGTAAATGAGTAAATGAAGGAATGATTATTCCTTGCTTTAGAACTTCTGGAATTAGAGGACAATATTAATAATACCATCGCACAGTGTTTCTTTGTTGTTAAT"| __truncated__

nchar(my_dna)

## [1] 140

my_dna_list <- strsplit(x = my_dna, split = "", fixed = TRUE)
length(my_dna_list)

## [1] 1

class(my_dna_list)

## [1] "list"

my_dna_vector <- unlist(my_dna_list)
length(my_dna_list[[1]])

## [1] 140

str(my_dna_vector)

##  chr [1:140] "A" "A" "C" "G" "A" "A" "T" "G" "A" "G" "T" "A" "A" "A" "T" "G" "A" "G" "T" "A" ...

length(my_dna_vector)

## [1] 140

# unique characters
unique(my_dna_vector)

## [1] "A" "C" "G" "T"

# number of As
(my_dna_vector == "A")

##   [1]  TRUE  TRUE FALSE FALSE  TRUE  TRUE FALSE FALSE  TRUE FALSE FALSE  TRUE  TRUE  TRUE FALSE
##  [16] FALSE  TRUE FALSE FALSE  TRUE  TRUE  TRUE FALSE FALSE  TRUE  TRUE FALSE FALSE  TRUE  TRUE
##  [31] FALSE FALSE  TRUE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
##  [46] FALSE FALSE  TRUE FALSE  TRUE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE  TRUE
##  [61] FALSE FALSE  TRUE FALSE  TRUE FALSE FALSE  TRUE FALSE  TRUE  TRUE FALSE  TRUE FALSE FALSE
##  [76]  TRUE  TRUE FALSE  TRUE  TRUE FALSE  TRUE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE  TRUE
##  [91] FALSE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
## [106] FALSE FALSE FALSE  TRUE  TRUE FALSE FALSE FALSE FALSE  TRUE FALSE  TRUE  TRUE FALSE  TRUE
## [121] FALSE  TRUE FALSE  TRUE  TRUE  TRUE FALSE  TRUE FALSE FALSE  TRUE  TRUE FALSE FALSE  TRUE
## [136] FALSE FALSE FALSE  TRUE FALSE

length(my_dna_vector[my_dna_vector == "A"])

## [1] 52

Frequency distribution

A gene consists of a sequence of nucleotides {A, C, G, T}.The number of each nucleotide can be displayed in a frequency table. This will be illustrated by the Zyxin gene which plays an important role in cell adhesion (Golub et al., 1999). The accession number (X94991.1) of oneof its variants can be found via an NCBI UniGene search. The code below illustrates how to install the package ape, to load it, to read gene ”X94991.1”of the species homo sapiens from GenBank, and to make a frequency table of the four nucleotides

# install.packages(c("ape"), repo="http://cran.r-project.org", dep=TRUE)
library(ape)
gene <- read.GenBank(c("X94991.1"),  as.character=TRUE)
table(gene)

## gene
##   a   c   g   t 
## 410 789 573 394

pie(table(gene))