Optimize codons and check before ordering

Codon Optimization rewrites a coding sequence for a host without changing the protein. The pre-order check flags regions that often slow down or raise the cost of DNA synthesis.

Optimize one coding sequence

1. Open the plasmid. Press Ctrl/Cmd+K and run Codon Optimization.
2. Choose a plasmid and a coding sequence, or paste one into Sequence to optimize.
3. Pick a Target Organism and an Optimization Strategy: Maximize expression, Balance codons or Minimize repeats.
4. Optionally open Advanced Settings to set Rare Codon Threshold, Enforce GC Content Window and Motifs to Avoid.
5. Click Optimize Sequence. Review GC content, rare codons and each codon change.
6. Click Apply optimization to write it into the plasmid, or Download Report.

Host choices: E. coli, S. cerevisiae, generic mammalian cells, human, mouse, fruit fly, C. elegans and B. subtilis.

Optimize many sequences

1. Click Batch at the top of Codon Optimization.
2. Set the target organism and strategy once. They apply to every row.
3. Add each coding sequence with Target.
4. Click Optimize N sequences, then Download batch.

Run a pre-order check

1. Open the plasmid.
2. Click Pre-order check in the plasmid header.
3. The report opens in a new tab and is saved to the plasmid's project.

The check covers seven signals: