Custom codon frequency tables

You can edit the list of codon frequency tables used by CLC Genomics Workbench.

Note! Please be aware that this process needs to be handled carefully, otherwise you may have to re-install the Workbench to get it to work.

In the Workbench installation folder under res, there is a folder named codonfreq. This folder contains all the codon frequency tables organized into subfolders in a hierarchy. In order to change the tables, you simply add, delete or rename folders and the files in the folders. If you wish to add new tables, please use the existing ones as template. In existing tables, the "_number" at the end of the ".cftbl" file name is the number of CDSs that were used for calculation, according to the site.

When creating a custom table, it is not necessary to fill in all fields as only the codon information (e.g. 'GCG' in the example below) and the counts (e.g. 47869.00) are used when doing reverse translation:

Name: Rattus norvegicus GeneticCode: 1 Ala GCG 47869.00 6.86 0.10 Ala GCA 109203.00 15.64 0.23 ....

In particular, the amino acid type is not used: in order to use an alternative genetic code, it must be specified in the 'GeneticCode' line instead.

Restart the Workbench to have the changes take effect.