Codon usage refers to the frequency at which different codons appear in an organism's genome. Different organisms show preferences for certain codons over others that code for the same amino acid, known as codon bias.

Understanding codon usage is crucial for:
• Optimizing gene expression
• Designing synthetic genes
• Improving protein production
• Understanding evolutionary relationships
• Predicting gene expression levels

1. Enter your DNA sequence
2. Select a model organism (or custom)
3. Click calculate to analyze:
• Codon frequency
• Amino acid composition
• Rare codon usage
• GC content
• Sequence optimization suggestions

• Codon Frequency: Shows how often each codon appears
• Relative Usage: Compares usage to organism's preference
• Rare Codons: Identifies potentially problematic codons
• Optimization Score: Indicates expression efficiency

• Avoid rare codons at the start of the gene
• Maintain balanced GC content
• Consider mRNA secondary structure
• Check for repetitive sequences
• Verify restriction enzyme sites
• Balance optimization with other factors