The 'effective number of codons' used in a gene

Abstract

A simple measure is presented that quantifies how far the codon usage of a gene departs from equal usage of synonymous codons. This measure of synonymous codon usage bias, the 'effective number of codons used in a gene', N̂c, can be easily calculated from codon usage data alone, and is independent of gene length and amino acid (aa) composition. N̂c can take values from 20, in the case of extreme bias where one codon is exclusively used for each aa, to 61 when the use of alternative synonymous codons is equally likely. N̂c thus provides an intuitively meaningful measure of the extent of codon preference in a gene. Codon usage patterns across genes can be investigated by the Nc-plot: a plot of N̂c vs. G + C content at synonymous sites. Nc-plots are produced for Homo sapiens, Saccharomyces cerevisiae, Escherichia coli, Bacillus subtilis, Dictyostellium discoideum, and Drosophila melanogaster. A FORTRAN77 program written to calculate N̂c is available on request. © 1990.