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Cubar: a versatile package for codon usage bias analysis in R.

Mengyue Liu1, Bu Zi2, Hebin Zhang3

  • 1College of Ecology, Lanzhou University, Lanzhou 730000, China.

Genetics
|September 26, 2025
PubMed
Summary

We developed cubar, a flexible R package for codon usage bias analysis. It addresses limitations of existing tools, offering efficient analysis and gene optimization for biological insights.

Keywords:
coding sequencecodon usage biascodon usage indexsequence analysissoftware

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Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Codon usage bias, the non-uniform use of synonymous codons, is a key biological phenomenon.
  • It is influenced by mutation, drift, and selection, impacting translation speed, accuracy, and mRNA stability.
  • Existing codon usage bias analysis tools lack flexibility and efficiency, failing to integrate recent research.

Purpose of the Study:

  • To introduce the Codon Usage Bias Analysis in R (cubar) package.
  • To provide a modular, user-friendly, and efficient tool for analyzing codon usage bias.
  • To incorporate advanced features like sliding-window analysis, differential usage assessment, and gene optimization.

Main Methods:

  • Development of the cubar R package.
  • Implementation of modular functions for calculating codon usage indexes.
  • Integration of sliding-window analyses, differential gene set analysis, and codon usage optimization algorithms.

Main Results:

  • Cubar offers a highly modular and user-friendly interface for codon usage bias analysis.
  • The package efficiently analyzes millions of coding sequences on a standard laptop within minutes.
  • Cubar supports advanced analyses including sliding-window, differential usage, and gene optimization.

Conclusions:

  • Cubar enhances the analysis of codon usage bias with its flexibility, efficiency, and advanced features.
  • This R package addresses the limitations of existing tools, facilitating deeper biological insights.
  • Cubar empowers researchers to explore codon usage patterns and optimize gene sequences effectively.