The Codon Bias Databse
Welcome to the Codon Bias Database! This database is a collection of metrics for the analysis of codon bias within the highly expressed genes of numerous bacterial organisms and strains.
Three metrics are reported to date, the RSCU, NRSCU and HEG FB. All calculations are based upon the set of highly expressed genes (HEGs) for the strain. For more details, be sure to check out our page describing the metrics with reference to the work of Paul Sharp and collaborators.
In addition to the metrics (which are available for download), we have also included access to the table of highly expressed genes for each strain. The set of highly expressed genes includes up to 40 translational elongation factors and ribosomal proteins (see Metrics). Also available for download are the nucleotide and amino acid sequences of these highly expressed genes so you can easily perform your own custom analyses.
Results are presented by genus facilitating comparison of the biases present amongst strains.
At present (June 2011), the CBDB includes over 300 strains representative of 17 genera. We will be updating and adding genera over the course of the next few months. You may notice a few strains missing for a genus. This is because the genomes are not fully annotated and as such only a few of the HEG are identifiable. We automatically generate the HEG protein tables and manually inspect them to ensure the most complete set of HEGs are used for our computations.
All calculations are performed using in-house software.
Questions/comments? Email cputonti [at] luc [dot] edu