Custom codon usage tables can be created in Geneious Prime 2019 onwards by importing one of two file formats:
- EMBOSS cusp (*.cusp)
- GCG CodonFrequency (*.cod).
These files can be acquired from a number of sources:
- Run GCG CodonFrequency or EMBOSS cusp on the command line outside of Geneious.
- Copy from public databases, such as GCG format from https://www.kazusa.or.jp/codon. See below for a screenshot of how to do this.
- Copy from the results of an online tool, e.g. http://www.bioinformatics.org/sms2/codon_usage.html and http://www.bioinformatics.nl/cgi-bin/emboss/cusp.
Once imported into Geneious, codon usage tables appear as a document in your folders which can be moved, copied, renamed or deleted. Regardless of where they appear in your folders, all codon usage table documents will appear in the options for the Back Translate and Optimize Codons operations.
Note that Geneious imports the Number column from these formats and recalculates the other columns so the values may be different from the source database due to rounding. In particular, the Kazusa database always has a Fraction of 0 but Geneious fills in its value by recalculating from Number.