How it works: Load a PDB structure and sequence into your browser (locally), 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 Maximisation & Harmonisation
Two Approaches Maximisation: Replace codons with the single most common synonymous codon in the expression organism (not optimal for expression due to repetition, GC content, structural constraints, etc.). Harmonisation: Match codon rarity patterns between source and expression organisms (aims to preserve co-translational folding).
Results
Codon Usage Tables
Load 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.