Notes on “The Codon Adaptation Index”

September 30, 2008

The Codon Adaptation Index – a measure of directional synonymous codon usage bias, and its potential applications: Paul M. Sharp and Wen-Hsiung Li.

The gist: The authors developed a way to assign numbers to synonymous codon usage bias that is superior to existing metrics. This new metric, the CAI, can be used to predict other biological effects that are correlated with synonymous codon usage bias.

The index uses a reference set of highly expressed genes from a species to assess the relative merits of each codon, and a score for a gene is calculated from the frequency of use of all codons in that gene.

The CAI has an advantage in that it is comparable between genes in a species.

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