How it works: Upload a PDB structure and sequence, select an organism to see rare codons highlighted in red/orange. Differential mode compares rarity between two organisms - blue = becomes more common, red = becomes rarer in target organism.
Codon Rarity Colour Scale
Very rare (slow translation)Common (normal)
Becomes rarerNo changeBecomes more common
Codon Optimisation & Harmonisation
Two Approaches: Optimisation: Replace codons with the most common synonymous codons in the expression organism (maximises expression). Harmonisation: Match codon rarity patterns between source and expression organisms (preserves co-translational folding).
Results
Codon Usage Tables
Upload Custom Codon Table
Format: TSV file with columns: Codon, AminoAcid, Frequency (or Usage). The frequency should be between 0 and 1, representing the relative usage of each codon.