The codon usage plugin for isolate databases calculates the absolute and relative synonymous codon usage by isolate and by locus.
The function can be selected by clicking the ‘Codon usage’ link in the Analysis section of the main contents page.
Alternatively, it can be accessed following a query by clicking the ‘Codons’ button in the Analysis list at the bottom of the results table. Please note that the list of functions here may vary depending on the setup of the database.
Enter the ids of the isolate records to analyse - these will be already entered if you accessed the plugin following a query. Select the loci you would like to analyse, either from the dropdown loci list, and/or by selecting one or more schemes.
Click submit. The job will be submitted to the queue and will start running shortly. Click the link to follow the job progress and view the output.
Four tab-delimited text files will be created.
- Absolute frequency of codon usage by isolate
- Absolute frequency of codon usage by locus
- Relative synonymous codon usage by isolate
- Relative synonymous codon usage by locus