Codon Optimization Tool
Optimize a protein or CDS for expression in E. coli, human, yeast, CHO, Pichia and more.
Codon-optimize a protein or coding DNA sequence for expression in E. coli, human, yeast, CHO, Pichia and more using most-frequent-codon usage tables. A useful starting point when designing a synthetic gene or boosting recombinant protein expression — then refine with GC, repeat and secondary-structure checks before synthesis.
Auto-detect reads anything >90% ACGTUN as DNA — force “Protein” for a peptide built only from Ala/Cys/Gly/Thr/Asn.
Result appears hereOptimization picks the most frequent codon per residue for the chosen organism. Usage tables are reference approximations (Kazusa-derived); verify against your expression system for critical constructs.
Design, edit, and verify complete constructsSeqStudio combines sequence editing and annotation, plasmid maps, primer/cloning/CRISPR design, Sanger verification, and GenBank/SnapGene files in one workspace.
How to use the Codon Optimizer tool
- 1Paste a protein sequence or a coding DNA sequence.
- 2Choose the target expression organism (E. coli, human, yeast, CHO, Pichia and more).
- 3Copy the optimized coding sequence and review its GC content.
Frequently asked questions
How does the optimization work?
For each amino acid, the most frequently used codon in the target organism is selected. Codon usage tables are reference approximations derived from the Kazusa database.
Can I paste DNA instead of protein?
Yes. If the input looks like a nucleotide sequence it is translated (frame +1, to the first stop) before optimization. The guess is made from the alphabet, so a genuine peptide made only of Ala, Cys, Gly, Thr and Asn reads as DNA — over the API, set inputType to "protein" or "dna" to force the interpretation instead of relying on the default "auto".
Should I rely on this for ordering a gene?
Treat it as a starting point. Real optimization also considers GC content windows, secondary structure, repeats and restriction sites — verify before synthesis.