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 (suspected slower 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 (aims to opreserve co-translational folding).
Results
Codon Usage Tables
Upload Custom Codon Table
Format:
TSV file
Columns: Codon | AminoAcid | Frequency The frequency should be between 0 and 1, representing the relative usage of each codon per target amino acid.