Measuring Codon Bias


Effective Codon Number (Nc) is a good overall measure
Runs on an intuitive scale from 20-61
Independent of gene length and amino acid composition
Does not require knowledge of 'preferred' codon set
Can be calculated from codon usage tables
A single measure, not a large table
Comparisons across species are possible
Can be plotted against other variables

However,
Not always accurate for short genes
Can detect bias, but not direction of bias

(Wright F. (1990) The 'effective number of codons' used in a gene. Gene 87:23-29)