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COUSIN (COdon Usage Similarity INdex): A Normalized Measure of Codon Usage Preferences
Jérôme Bourret1, Samuel Alizon1, Ignacio G Bravo1
1Centre National de la Recherche Scientifique, Laboratory MIVEGEC (CNRS, IRD, Uni Montpellier), Montpellier, France.
Genome Biology and Evolution
|December 5, 2019
Summary
We developed COUSIN, a new index to measure codon usage similarity between genes or genomes. This tool precisely reveals codon usage patterns, like bimodal distributions in human and chicken genes.
Area of Science:
- Genomics and Bioinformatics
- Molecular Biology
Background:
- Codon Usage Preferences (CUPrefs) reflect non-random synonymous codon selection across genomes.
- Existing indices for evaluating CUPrefs have limitations in interpretation and normalization.
Discussion:
- COUSIN (COdon Usage Similarity INdex) offers a normalized comparison of CUPrefs against a reference, accounting for random codon usage.
- The index provides quantitative and qualitative interpretations, enhancing the understanding of CUPrefs.
Key Insights:
- COUSIN precisely identifies a bimodal distribution in human and chicken gene CUPrefs, a novel finding.
- The COUSIN index facilitates the discovery of genome-specific CUPrefs.
Outlook:
- The COUSIN software enables comprehensive CUPrefs analysis, including statistical assessments and gene expression optimization.
- This user-friendly tool opens new avenues for exploring genomic sequence characteristics and evolutionary pressures.