Codon Usage Calculator
Paste a coding sequence to tabulate how often each codon is used — total counts, frequency per 1000 codons, and the fraction each codon makes up among the synonymous codons for its amino acid. The sequence is read in frame 1; U is treated as T.
Paste a coding sequence above to see its codon usage.
How it works
Codon usage describes how often each of the 61 sense codons (and the 3 stop codons) is used to encode a protein. Because most amino acids are specified by more than one codon, organisms and highly expressed genes tend to favour particular synonymous codons — a bias that matters for gene expression and for optimising synthetic genes.
This calculator reads your sequence in frame 1, three bases at a time, and counts each codon. For every codon it reports the raw count, the frequency per 1000 codons, and the fraction it represents among the synonymous codons for the same amino acid. Paste a single coding sequence; FASTA headers, spaces and numbers are ignored and U is read as T.
Examples
- A sequence of ATG repeats shows ATG (Met) at a fraction of 1.00.
- Frequency per 1000 lets you compare codon use between sequences of different length.
- The fraction column reveals synonymous codon preference within each amino acid.
Frequently asked questions
- What is codon usage bias?
- It is the unequal use of synonymous codons — codons that encode the same amino acid. Genomes and highly expressed genes often prefer particular codons that match abundant tRNAs.
- What does frequency per 1000 mean?
- It normalises the raw count to a rate per 1000 codons, so you can compare codon usage between sequences of different lengths.
- What is the fraction column?
- It is the proportion of a codon among all synonymous codons for its amino acid. If leucine is encoded 10 times and CTG accounts for 4 of them, CTG's fraction is 0.40.
- Which reading frame is used?
- The sequence is read in frame 1, starting at the first base. Make sure your input is a coding sequence in frame — for example beginning at the start codon.