Codon Optimizer

Use this free online codon optimization tool to adapt a DNA CDS or protein input to an expression host while preserving the translated amino acid sequence and reporting GC content, codon changes, and downstream primer design options.

Codon optimizer inputs
Tool mode
Codon usage tables are embedded from Kazusa/CUTG. Cell-line hosts use organism-level approximations.
No sequence loaded.

Accepted file types: .txt, .fa, .fasta, .fna, .ffn, .seq, .gb, .gbk, .genbank. Plain-text DNA, FASTA, or GenBank text only.

Circular DNA/plasmids are not handled as circular yet. For regions that cross base 1, paste the relevant region as linear FASTA or raw DNA sequence.

Leave blank to optimize the full coding sequence, or enter a range, e.g. 3-995.

Select enzymes from the search suggestions or type exact DNA motifs. Multiple entries are comma-separated. The optimizer will try synonymous codon swaps where possible and report any remaining sites.

References

References for codon optimization logic: Codon Adaptation Index concepts, host codon usage tables, Kazusa/CUTG-style codon-frequency data, translation checks, reverse translation, and GC-content constraints. Mol Biology Tools implementation code is original.

  1. Host-adaptation scoring concept: Sharp and Li (1987), Codon Adaptation Index.
  2. Codon-usage table basis: Nakamura, Gojobori, and Ikemura (2000), codon usage tables from sequence databases.
  3. Embedded host codon-usage reference data: Kazusa Codon Usage Database.
  4. Translation checks and reverse-translation constraints: NCBI Genetic Codes table.