SeqBench
Sequence stats, reverse complement, six-frame translation, ORFs, and motif search.
CodonBench: codon optimization for expression
CodonBench redesigns a gene's codons to suit your expression host while keeping the protein identical, and reports the codon adaptation index, GC content, and rare codons before and after.
Free, no sign-up, and installable on your phone. Runs in your browser at codons.gataca.com.
What you can do with CodonBench
- Prepare a gene for synthesis and expression in E. coli
- Move a human or viral gene into yeast or mammalian cells
- Remove restriction sites you need for cloning
- Find rare codons that may slow translation
How to use it
- Paste a protein sequence or a coding DNA sequence.
- Choose the expression host and the optimization method.
- List any restriction sites to keep out of the design.
- Copy the verified, optimized DNA and compare CAI and GC with the original.
Features
- Codon usage tables for E. coli, S. cerevisiae, and human
- Most-frequent and usage-matched optimization
- Codon Adaptation Index (CAI) before and after
- Rare codon highlighting
- Restriction site removal
- Automatic check that the protein is unchanged
- Save results as reports, spreadsheets, or sequence files
- Install it on your phone or computer; works offline
Frequently asked questions
Which method should I choose?
Match host usage is usually the better default because it avoids repetitive sequence while skipping rare codons. Most frequent codon maximizes CAI when that matters more.
Why does changing the seed give a different sequence?
Usage-matched optimization chooses among good codons at random in proportion to host usage. The seed makes each design reproducible.
Can I add another organism?
Not yet. Contact us if you need a specific host; we can add its codon usage table.
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Need CodonBench to do more?
We build custom versions and full pipelines for research teams.