CBDB: The Codon Bias Database

About the Metrics...

For each of the strains available, three codon usage metrics are presented. All of these values are calculated based upon the codon usage within the set of highly expressed genes (HEGs). The set of highly expressed genes (available for download for each of the strains by selecting the link "Download HEG Protein List" include the set of genes encoding translation elongation factors Tu (tufA), Ts (tsf) and G (fusA) in addition to 37 ribosomal proteins (rplA-rplF, rplI-rplT, and rpsB-rpsT). These 40 genes in total are the same set of highly expressed genes selected by Sharp et al. (2005) in their work calculating the strength of selected codon usage bias.

The first value reported is the RSCU or relative synonymous codon usage value. The RSCU value is the observed frequency of the codon divided by the frequency expected under the assumption that each synonymous codon is used equally (Sharp et al. 1986). The RSCU values reported can be used to calculate the codon adaptation index for any gene present within the strain's genome following the method presented by Sharp and Li (1987). The RSCU values range from 0 to the number of synonymous codons for the codon's amino acid.

The second value reported is the NRSCU or normalized relative synonymous codon usage value. This metric is equivalent to the RSCU value divided by the number of synonymous codons for the codon's amino acid. Thus each codon has a value between 0 and 1. This value maintains the unequal distribution (bias) of the usage of codons within the HEGs but each amino acid is equally weighted.

The final value reported is referred to as the "HEG FB" value. This value represents the frequency of the appearance of a particular codon amongst all of the codons which appear in the HEGs.

The amino acid (AA) is listed for each codon using the one-character abbreviation. The termination codons are indicated as AA "X".


References:

  • Sharp PM, Bailes E, Grocock RJ, Peden JF, Sockett RE. 2005. Variation in the strength of selected codon usage bias among bacteria. Nucleic Acids Research 33, 1141-1153. [PubMed]
  • Sharp PM, Li W-H. 1987. The codon adaptation index - a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Research 15, 1281-1295. [PubMed]
  • Sharp PM, Tuohy TM, Mosurski KR. 1986. Codon usage in yeast: cluster analysis clearly differentiates highly and lowly expressed genes. Nucleic Acids Research 14, 5125-5143. [PubMed]