Rare Codon Analysis

Identify rare codons in DNA sequences for optimized protein expression

Analysis Summary

Total Codons
0
Rare Codons (<10%)
0
Low Usage (10-30%)
0
CAI Score
0.00

Codon Usage Details

PositionCodonAmino AcidFrequency (%)Status

What is Rare Codon Analysis?

Rare codon analysis identifies codons that are infrequently used in your expression host organism. These rare codons can significantly reduce protein expression levels and cause translation pausing.

How to Use This Tool

  1. Select your expression host organism
  2. Paste your DNA coding sequence
  3. View rare and low-usage codons
  4. Check CAI score for expression prediction

When to Use

  • Before cloning genes for heterologous expression
  • Optimizing protein production yields
  • Troubleshooting low expression
  • Designing synthetic genes

Codon Usage Categories

Rare: <10% frequency (avoid)
Low: 10-30% frequency (caution)
Common: >30% frequency (preferred)
CAI: 0.0-1.0 (higher is better)

Expression Hosts

Different organisms have distinct codon preferences:

  • E. coli: Bacterial expression
  • Yeast: Eukaryotic, easy culture
  • CHO/Human: Mammalian proteins
  • Insect: Baculovirus system

FAQ

Q: What is CAI?
A: Codon Adaptation Index (0-1) predicts expression level based on codon usage.

Q: Should I optimize all rare codons?
A: Focus on clusters of rare codons and the N-terminal region for best results.