Codon Optimizer

Optimize a coding DNA sequence while preserving the translated protein sequence and checking codon-level changes.

Codon Optimizer is a browser-based tool for changing codon usage while preserving the translated protein sequence and checking GC content.

Use note: Send optimized CDS to Primer Designer for downstream primer design after checking restriction sites.

Input mode

Expression host

Codon usage tables are embedded from Kazusa/CUTG. Cell-line hosts use organism-level approximations.

DNA CDS sequence or FASTA

No sequence loaded.

Upload sequence file (optional)

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.

Optimization region (optional)

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

Minimum GC%, target range

Maximum GC%, target range

Avoid restriction sites or motifs (optional)

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.