centralDogma

About

The centralDogma package simulates the central dogma of molecular biology: DNA -> RNA -> Peptide. The package provides functions for each step and also a function to plot the abundance of each amino acid in a peptide.

Installation

devtools::install_github("r4bds/centralDogma")

Usage

library("centralDogma")

Create a random DNA strand

Normally, you have a DNA strand of your own you want to investigate, but a random strand can be generated.

dna_strand <- random_dna(dna_length = 6000)

Transcribe DNA into RNA

The first step of the central dogma is to transcribe a gene (DNA strand) into RNA

rna_strand <- transcribe(dna = dna_strand)

Split RNA strand into a list of codons

In reality, some post transcriptional changes occur to the messenger RNA, but we will ignore that fact here. To properly translate the RNA, it needs to be converted into a list of codons.

codons <- codon_split(rna = rna_strand)

Translate codons into a peptide

The list of codons can then be translated using the codon_table provided with the package. Run ?codon_table if you want more information.

peptide <- translate(codons = codons)

A lot of post-translational changes are performed to the peptide, but this package will not apply those.

You are free to explore the created peptide. Here, a function is provided that plots the abundance of each amino acid in the peptide.

Plot the abundance of each amino acid in a peptide

plot_abundance(peptide = peptide) +
  ggplot2::theme(legend.position = "none")