RSCU Calculator
Compute the Relative Synonymous Codon Usage (RSCU) of a coding sequence. RSCU measures how often a codon is used compared with what you'd expect if all synonymous codons for its amino acid were used equally — values above 1 are favoured, below 1 are avoided.
Paste a coding sequence above to compute RSCU.
How it works
Relative Synonymous Codon Usage (RSCU) normalises codon counts so that codon preference can be compared independently of amino-acid composition. For each codon, RSCU is the observed number of occurrences divided by the number expected if every synonymous codon for that amino acid were used equally. It equals the count times the number of synonymous codons, divided by the total count for that amino acid.
An RSCU of 1 means the codon is used exactly as often as expected. Values above 1 mark over-represented (preferred) codons and values below 1 mark under-represented ones; codons for amino acids with a single codon (Met, Trp) are always 1. Paste a coding sequence read in frame 1 — over-represented codons are highlighted.
Examples
- Equal use of two synonymous codons gives RSCU 1.0 for each.
- If AAA is used three times and AAG once (both Lysine), RSCU is 1.5 and 0.5.
- Methionine (ATG) and tryptophan (TGG) always have RSCU 1 — they have no synonyms.
Frequently asked questions
- What is RSCU?
- Relative Synonymous Codon Usage is the ratio of a codon's observed frequency to its expected frequency under equal synonymous usage. It reveals codon preference independent of amino-acid content.
- How is RSCU calculated?
- RSCU = (observed count × number of synonymous codons for the amino acid) ÷ (total count of all codons for that amino acid). A value of 1 means no bias.
- What do values above or below 1 mean?
- Above 1 means the codon is used more than expected (over-represented or preferred); below 1 means it is used less than expected (under-represented). Exactly 1 means it matches the unbiased expectation.
- Why are some codons always 1?
- Amino acids encoded by a single codon — methionine (ATG) and tryptophan (TGG) — have no synonymous alternatives, so their RSCU is always 1.