In rforbiodatascience22/group_16_package: What the Package Does (One Line, Title Case)

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

library(CentralDogma)

Description

This packages consists of five functions which together generates a random DNA sequence, transcribe it to mRNA, translate it to protein and finally visualize the occurrence of each aminoacid in the sequence.

generate_dna()

This function takes an integer (the wanted length of the DNA sequence) as input, and generates a random string of A, T, C and G (DNA sequence) with that length as output.

Example:

sample_DNA <- generate_dna(60)
sample_DNA

mRNA()

Takes a string (DNA sequence) as input, change each T to an U, and return the DNA sequence with the changes.

Example:

sample_mRNA <- mRNA(sample_DNA)
sample_mRNA

make_codons()

Takes a string (mRNA sequence) as input, and the start position for translation, default start is 1. The function then split the mRNA sequence into a vector of strings (codons of 3 nucleotides) as output.

Example:

sample_codons <- make_codons(sample_mRNA, start = 1)
sample_codons

translation()

A vector of strings symbolizing triplets of 3 nucleotides (codons) are given as input, each codon is translated using the codon table to the correct amino acid, and the amino acid sequence is returned as a string where each letter represents an amino acid.

Example:

sample_peptide <- translation(sample_codons)
sample_peptide

visualize_aa_counts

The function takes a string (sequence of single letter amino acids) as input and returns a plot showing the counts of each of the amino acid in the input sequence.

Example:

visualize_aa_counts(sample_peptide)

Combined workflow

The functions can be strung together with pipes to make a complete workflow:

DNA_length <- 60

generate_dna(DNA_length) %>% 
  mRNA() %>% 
  make_codons() %>% 
  translation %>% 
  visualize_aa_counts()

Usage cases of the package

The first function of the package, generate_DNA(), can be considered a helper function which is used to generate a random DNA sample to illustrate the functions of the other 4 functions. The idea is that you can take a DNA sequence (or mRNA sequence if that is your starting point) and generate the amino acid sequence it would result is. That is, you want to use it with coding sequences where the introns have already been removed. Getting the amino acid sequence can then be used to investigate the function of the protein product of the given DNA/mRNA sequence by looking at conserved regions through alignment to online databases.

Further additions to the package

An obvious addition would be a function to search for potential translational start sites (ATG/AUG) in the sequence and the length of the protein they would result in. This could assist in establishing the most likely reading frame. Another potential funtion, albeit harder to implement, would be one which helps find likely intron/exon structures in a raw DNA sequence. Even a fairly simple implementation would likely have to compare the sequence against a database to find conserved regions, as exons an be expected to be more conserved (except in the case where a promoter region is found in an intron etc.)

rforbiodatascience22/group_16_package documentation built on April 6, 2022, 11:19 a.m.