Codon Bias

Codon bias was estimated using two measures: the effective number of codons (ENC; Wright 1990) and the frequency of optimal codons (Fop; Ikemura 1981). For ENC, lower values indicate stronger synonymous codon usage bias, while for Fop higher values indicate stronger bias. Both measures were calculated using the CodonW program. For genes with multiple transcripts encoding proteins of different lengths, the longest coding sequence was used. For more details, see Hambuch and Parsch (2005).

Ikemura T., Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: a proposal for a synonymous codon choice that is optimal for the E. coli translational system, (J. Mol. Biol. 151: 389-409; 1981).

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

Hambuch T.M., Parsch J., Patterns of synonymous codon usage in Drosophila melanogaster genes with sex-biased expression, (Genetics 170: 1691-1700; 2005).