Codon Adaptation Index (CAI) Calculator & Codon-Usage Analyzer
Score a coding sequence's codon usage against an expression host, before optimising.
🔒 Local processing — pasted sequences are not uploaded
Before you codon-optimise, find out how well your sequence already matches the host. Paste a coding sequence and pick an expression organism; the tool computes the Codon Adaptation Index (CAI), the %GC at third positions, and a per-codon adaptiveness chart that highlights rare codons which can stall translation. If the score is low, hand off to the Codon Optimizer in one click.
0 bp
No complete codons found in this frame.
The Codon Adaptation Index (CAI) is the geometric mean of each codon’s relative adaptiveness (w = its frequency ÷ the most-frequent synonymous codon) in the chosen host, excluding Met/Trp and stops. GC3 is the GC content at third codon positions. Run this before deciding whether to codon-optimise.
How to use the Codon Adaptation Index tool
- 1Paste a coding sequence (starting at ATG) and choose the expression host.
- 2Read the CAI, GC3 and the per-codon adaptiveness chart (red bars are rare codons).
- 3If needed, click through to the Codon Optimizer to improve it.
Frequently asked questions
- What is a good CAI value?
- CAI ranges from 0 to 1; higher means codons closer to the host's most-frequent choices. Highly expressed genes often sit around 0.7–1.0, and values below ~0.5 suggest codon optimisation may help — though CAI is only one factor in expression.
- How is CAI calculated here?
- As the geometric mean of each codon's relative adaptiveness (its frequency divided by the most-frequent synonymous codon) in the chosen host, excluding single-codon amino acids (Met, Trp) and stop codons. Never-used codons are floored to avoid a zero product.
- Which organisms are supported?
- E. coli, human and yeast codon-usage tables, the same ones used by the Codon Optimizer.