Codon Adaptation Index Calculator

The Codon Adaptation Index (CAI) measures how closely the codon usage of a gene matches the preferred codon usage of a reference set of highly expressed genes. It is the geometric mean of the relative adaptiveness (w) values of all codons in the gene. CAI ranges from 0 to 1; values near 1 indicate strong bias toward the most-used codons, which often correlates with higher expression.

CAI is the geometric mean of the per-codon relative adaptiveness values: CAI = (product of w_i)^(1/L), equivalently exp of the average of the natural logs of w. Here L is the number of codons scored (start and stop codons and single-codon amino acids are usually excluded) and each w is that codon's frequency relative to the most frequent synonymous codon in the reference set.

For each codon, w is its usage frequency in the reference set divided by the frequency of the most-used synonymous codon for that amino acid. The most-preferred codon for each amino acid therefore has w = 1, and rarer synonyms have w less than 1. The reference set is typically a group of highly expressed genes from the organism of interest.

CAI uses the geometric mean because relative adaptiveness values are multiplicative ratios. The geometric mean is the natural average for ratios and prevents a single very small w from dominating less than it would in a product, while still penalising rare codons more than an arithmetic mean would. It also keeps CAI bounded between 0 and 1.

Enter the number of codons scored and the sum of the natural logarithms of their relative adaptiveness values, or use the per-codon helper to combine several w values. CAI = exp(sum of ln w divided by number of codons). Because the w table is organism-specific, you supply the values; this tool performs the deterministic geometric-mean computation.