The Codon Usage Analysis tool calculates the frequency and relative usage of all 64 codons in a DNA or RNA sequence. This analysis is essential for understanding:
- **Codon bias**: Preferential use of certain codons over others - **Gene expression patterns**: Different organisms prefer different codons - **Sequence optimization**: Designing sequences for optimal expression - **Evolutionary studies**: Codon usage patterns reflect evolutionary history
Supported formats
- Raw DNA/RNA sequence (ATGC characters) - FASTA format (with or without header)
Sequence requirements
- Must contain only valid nucleotide characters: A, T, G, C (DNA) or A, U, G, C (RNA) - Case insensitive - Minimum length: 3 nucleotides (to form at least one codon)
Example input
``` ATGCGATCGATCGATCGATCGATCGATCGATCGATCGATCG ```
Or FASTA format: ``` >sequence1 ATGCGATCGATCGATCGATCGATCGATCGATCGATCGATCG ```
The tool provides comprehensive codon usage statistics:
For each codon
- **Amino Acid**: The amino acid encoded by the codon - **Count**: Number of times the codon appears in the sequence - **Relative Usage**: Usage frequency relative to other codons for the same amino acid - **Percentage**: Percentage of total codons represented by this codon
Key metrics
- Total codons analyzed - Codon usage distribution - Most and least frequently used codons - Amino acid composition
**1. Gene Expression Optimization** - Identify rare codons that may slow translation - Optimize sequences for heterologous expression - Design synthetic genes with preferred codon usage
**2. Evolutionary Analysis** - Compare codon usage patterns across species - Study evolutionary pressures on gene sequences - Analyze codon adaptation index (CAI)
**3. Functional Genomics** - Understand gene expression regulation - Study translation efficiency - Analyze genetic code usage patterns
1. **Complete sequences**: Use complete coding sequences (CDS) for accurate analysis 2. **Remove introns**: Ensure input sequences contain only exonic regions 3. **Check reading frame**: Start sequences at the correct start codon (ATG) 4. **Compare references**: Compare results with organism-specific codon usage tables 5. **Consider context**: Codon usage varies by gene function and expression level