CAI

CAI codon adaptation index

cai calculates the Codon Adaptation Index. This is asimple, effective measure of synonymous codon usage bias.

The index uses a reference set of highly expressed genes from a speciesto assess the relative merits of each codon, and a score for a gene iscalculated from the frequency of use of all codons in that gene. Theindex assesses the extent to which selection has been effective inmoulding the pattern of codon usage. In that respect it is useful forpredicting the level of expression of a gene, for assessing theadaptation of viral genes to their hosts, and for making comparisons ofcodon usage in different organisms. The index may also give anapproximate indication of the likely success of heterologous geneexpression.