Codon Optimizer
Codon optimization for host-specific protein expression
Tool Guide
Definition
Codon optimization tool — From a protein amino acid sequence or CDS DNA, re-encodes using the highest-frequency codons of the host (E.coli / CHO / HEK293·Human / Mouse). Evaluates fit with CAI (Codon Adaptation Index) = (∏ wᵢ)^(1/L). Supports dual-host mode and restriction site avoidance.
Purpose
(1) Recombinant protein expression — optimize a native human gene for E.coli BL21 → 5–10× higher yield (2) CHO/HEK293 mammalian expression (e.g., monoclonal antibody, recombinant protein) (3) Balance GC% and remove repeats before gene synthesis ordering (4) Dual-host (E.coli production + mammalian assay) compatible sequences
How to Use
① Input mode (Protein 1-letter code or CDS DNA) ② Choose host (E.coli / CHO / Human / Mouse — or dual-host) ③ Options • Restriction sites to avoid (EcoRI, BamHI, etc.) • Max GC% • Repeat avoidance (remove ≥8 nt identical stretches) ④ Output: • Optimized DNA sequence • Original CAI vs Optimized CAI • GC% distribution (sliding window) • Major codon-change hotspots
Examples
Example) Human IL-2 (153 aa) → optimized for E.coli BL21 expression → Input: protein sequence or native human CDS → Output CDS: 459 bp → Original CAI (E.coli): 0.45 → Optimized CAI: 0.92 → GC: 58% (within E.coli optimal 50–60%) → No EcoRI/BamHI sites (cloning-compatible) → Clone into pET28a (NdeI/XhoI) → ~8× expression boost expected