Codon Usage Analysis

Analyze codon usage patterns and frequencies in DNA sequences. Identify synonymous codon preferences and assess coding sequence optimization.

What is Codon Usage Analysis?

Codon usage analysis examines the frequency of synonymous codons in coding sequences. Different organisms prefer certain codons over others for the same amino acid, affecting protein expression levels and translation efficiency.

How to Use This Codon Usage Tool

Analyze codon patterns in three simple steps:

  1. Paste your coding DNA sequence (ORF or CDS)
  2. View automatic codon frequency analysis
  3. Download detailed results with synonymous codon usage

When to Use

This tool is useful when you need to:

  • Optimize sequences for heterologous expression
  • Analyze codon bias in genes or genomes
  • Compare codon usage between species
  • Identify rarely used codons for expression optimization

Example Input

Sample coding sequence:

ATGAAATCTGGAACTTCTGAGTCTTGGACCAAG...

Use the Example button to load a sample sequence.

Example Output

Analysis shows codon frequencies and preferences:

AmAcid Codon Number /1000 Fraction
Phe    TTT   6.00  28.30  0.75
Phe    TTC   2.00   9.43  0.25
Met    ATG   8.00  37.74  1.00

Each codon's count, frequency per 1000 codons, and fraction among synonymous codons (sample sequence one, 212 codons).

FAQ

Q: What genetic code is used?
A: Pick from 24 NCBI translation tables with the Genetic Code selector — Standard, vertebrate/invertebrate and yeast mitochondrial, bacterial/plastid, ciliate nuclear and more. Stop and reassigned codons follow the selected table.

Q: Can I analyze multiple sequences?
A: Yes, separate sequences with FASTA headers or line breaks.