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 uses a versioned FDA HIVE-CoCoPUTs snapshot (public service labelled September 2021; retrieved September 2026). 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 for the full CDS, or enter a codon-aligned range such as 4-300.

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

Sources for host codon usage, host-adaptation scoring, and standard-code translation. Optimization uses original Mol Biology Tools code and a fixed, reproducible data snapshot.

  1. Host-adaptation scoring concept: Sharp and Li (1987), Codon Adaptation Index. Scores here use the selected host's genomic codon frequencies, not a dedicated highly expressed gene reference set.
  2. Codon-usage database: Alexaki et al. (2019), Codon and Codon-Pair Usage Tables (CoCoPUTs).
  3. Host codon-usage data: FDA HIVE-CoCoPUTs, public service release September 2021. The source README identifies RefSeq 99 and GenBank 238.0. Our 20-host snapshot was retrieved on 14 September 2026; that is not the underlying database release date. Counts, taxa, individual source URLs, and checksums.
  4. Dataset scope: Species-level genomic CDS counts, excluding organelles. RefSeq tables are used where available; Nicotiana benthamiana uses a smaller GenBank fallback. Cell-line labels identify host-species approximations, not cell-line-specific expression tables. Codon-pair and tissue-specific CoCoPUTs tables are not used.
  5. Translation checks and reverse translation: NCBI standard genetic code, table 1.
  6. Sequence-file formats: NCBI FASTA documentation and GenBank sample record.