CAI (Codon Adaption Index) - (Sep/20/2006 )

Dear Freinds
Can any body tell me how to calculate the codon adaption index and how to interpret these values. can any body give some suggestion about it.
regards

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Try my tool CAI Calculator at http://www.evolvingcode.net/codon/cai/cai.php

You can also try John Peden's CodonW

I also have detailed explanation of this measurement. Email me if you have further questions.

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Hi,

The Codon Adaption Index measures how closely a codon of a specific gene matches the optimum codons used in a set of reference genes. Sharp and Li (1987) used a set of highly expressed genes in E. coli as their reference set, to determine if the codon used was correlated with gene expression. They showed that CAI was correlated with expression level in E. coli.

CAI is calculated from the equation:

CAI = (ΠWk)1/L

NOTE: 1/L is raised as a power (see attachment called CAI)

Where:

Wk = measure of the fitness of codon k relative to the reference set
CAI = geometric average of the fitness values of the codons used by the gene
L = total number of codons in the gene (This DOES NOT INCLUDE the stop codon, MET and TRP)

The problem with CAI is that it measures synonymous codon correspondence to a biased set of reference genes, but not codon bias itself. Therefore, genes with a low CAI may be highly biased, but simply biased towards codons which are not most frequent in the reference set.

A more direct measure of synonymous codon bias was proposed by Wright (1990) known as the ENC (Effective Number of Codons). This measures the effective number of codons by a method used in population genetics to determine the effective number of alleles segregating in a population. Each amino acid group is analogous to a locus and the synonymous codons are analogous to alleles. See attachment 2 (ENC) for the equation.

Anyway hope this helps

Good Luck!

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