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Sequence composition and bias analyses

This repository contains scripts to analyse the sequence composition and bias of protein and nucleotide (DNA) sequences.

Software requirements

Scripts are implemented in R v3.6, and use the following packages: seqinr, argparse, ggplot2, dplyr and tidyr.

Scripts

This repository contains five scripts, listed below. Each script can be run from the command line with custom input and output options. Use the help option (-h/--help) on each script to see all the available options.

Rscript script_name.R -h
  • bias_profile_dna.R: plot the nucleotide composition and bias profile along the DNA sequence of a gene.
  • bias_profile_prot.R: plot the amino acid composition and bias profile along a protein sequence.
  • composition_dna.R: analyse the DNA composition for a subset of genes, including GC content, nucleotide asymmetries and expected vs observed nucleotide frequencies, and generate PCA and dendogram plots.
  • composition_prot.R: analyse the amino acid composition for a subset of protein sequences, and generate PCA and dendogram plots.
  • dotplot.R: generate a dot-plot of two protein or DNA sequences.

Results

Each script takes as input a single or multiple protein sequences in a FASTA format, and other options and parameters, and produces figures and/or results tables. Results and figures for example input files are provided in the examples folder.

Reference

These scripts were created and used for my PhD research work at the European Bioinformatics Institute (EMBL-EBI). More details are provided in my Thesis (insert link when available).

Aleix Lafita - April 2021