How do I create a custom codon usage table?

Custom codon usage tables can be created in Geneious Prime 2019 by importing one of two file formats:

  • EMBOSS cusp (*.cusp)
  • GCG CodonFrequency (*.cod).

These files can be acquired from a number of sources:

codon-usage-copy-paste-2.png

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.

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