Codon optimizer & reverse translation

Convert a protein sequence (or an existing CDS) into DNA using species codon-usage tables. Optionally avoid common restriction sites, inspect GC along the gene, and export FASTA for ordering or cloning into CloneIT2.

Tables are approximate browser-friendly usage profiles (E. coli, human, mouse, yeast, insect). For publication-grade CUB metrics, compare against organism-specific datasets. All processing stays local.

Avoid restriction sites (optional)

Run optimization to reverse-translate and score GC / restriction sites.

How this tool works

For each amino acid the tool chooses a synonymous codon from the selected host table — either the most frequent codon or a frequency-weighted random draw. When enzymes are checked, it retries synonyms to reduce recognition sites spanning codon junctions.

CAI and GC

Approximate CAI compares each chosen codon to the most frequent synonym in the same table. The GC plot uses sliding windows (~40 bp) across the optimized CDS.

Limitations

  • Does not model secondary structure, rare Arg clusters, or IRES/splice motifs.
  • Cannot guarantee removal of every selected cutter if synonymous options are limited.
  • Sequences never leave your browser.