Additional file 2.

Calculation of Codon Usage Bias (CUB) – Explanation and Example. The 64 codons were sorted in to 21 subgroups (fractions) corresponding to the 20 coded amino acids and the stop signal. The sum of synonymous codon frequencies were always regarded as 100% i.e. the sum of all codon frequencies is 2100% (color coded columns). The fractional frequency (CUF_ij %) of a synonymous codon is the contribution of that codon to this 100%. The theoretical, natural frequencies of the synonymous codons is regarded as equal to each other (for example the natural fractional frequency of each synonymous codon of Arg is 100%/6 = 16.7%). The difference between this theoretical (calculated) frequency and the real (counted) fractional frequency of a codon is the CUB_ij %. However it is necessary to use the |CUB_ij %| value instead to be able to calculate and compare the total CUB values of entire proteins (i.e. the sum of 64 CUB values). A theoretical extreme case of codon usage is when only one of all synonymous codons is used (CUB% 1 max column). The maximal possible CUB of all codons will in this case be 2416.7%, which is regarded as the CUFmax. In the real case of Homo sapiens the sum of fractional frequencies is 456, which is 18.9% of the theoretical CUBmax.

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Biro Theoretical Biology and Medical Modelling 2008 5:16   doi:10.1186/1742-4682-5-16