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  • Director of Center
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© Research
Publication : Genome biology and evolution

COUSIN (COdon Usage Similarity INdex): A Normalized Measure of Codon Usage Preferences.

Scientific Fields
Diseases
Organisms
Applications
Technique

Published in Genome biology and evolution - 01 Dec 2019

Bourret J, Alizon S, Bravo IG

Link to Pubmed [PMID] – 31800035

Link to DOI – 10.1093/gbe/evz262

Genome Biol Evol 2019 Dec; 11(12): 3523-3528

Codon Usage Preferences (CUPrefs) describe the unequal usage of synonymous codons at the gene, chromosome, or genome levels. Numerous indices have been developed to evaluate CUPrefs, either in absolute terms or with respect to a reference. We introduce the normalized index COUSIN (for COdon Usage Similarity INdex), that compares the CUPrefs of a query against those of a reference and normalizes the output over a Null Hypothesis of random codon usage. The added value of COUSIN is to be easily interpreted, both quantitatively and qualitatively. An eponymous software written in Python3 is available for local or online use (http://cousin.ird.fr). This software allows for an easy and complete analysis of CUPrefs via COUSIN, includes seven other indices, and provides additional features such as statistical analyses, clustering, and CUPrefs optimization for gene expression. We illustrate the flexibility of COUSIN and highlight its advantages by analyzing the complete coding sequences of eight divergent genomes. Strikingly, COUSIN captures a bimodal distribution in the CUPrefs of human and chicken genes hitherto unreported with such precision. COUSIN opens new perspectives to uncover CUPrefs specificities in genomes in a practical, informative, and user-friendly way.