Synonymous Codon Sites

Count equally weighted synonymous single-base alternatives by codon position using the standard code.

Description

Synonymous alternatives preserve a codon’s amino acid.

Synonymous alternatives preserve a codon’s amino acid. Equal weighting of three possible substitutions at each position yields a fractional synonymous-site count.^[1]

Count equally weighted synonymous single-base alternatives by codon position using the standard code.

When to use Synonymous Codon Sites

Use this for the following task: Count equally weighted synonymous single-base alternatives by codon position using the standard code.

Prepare the observed records or explicit model parameters requested below. Keep probabilities as fractions and paired records aligned.

How to use Synonymous Codon Sites and understand its results

Prepare the observed records or explicit model parameters requested below. Keep probabilities as fractions and paired records aligned.
Enter codon using the field table, then run the tool.
Read synonymousFractionsByPosition, synonymousSiteCount, nonsynonymousSiteCount. Interpret flags, units, ordering and placeholder values using the rules below.
Review any reported issue or failed check, correct the supplied values when appropriate, and verify the result in its intended context.

Input field	Meaning	Value type and bounds	Requirement
codon	Codon	string	Required

Normalize a canonical sense codon and test all three replacement bases at each position under the standard code. Count same-amino-acid alternatives.^[2]

siteFraction[i] = synonymous single-base alternatives at i / 3; nonsynonymousSites = 3−sum(siteFractions)

This summarizes the declared operation. Units, indexing, inclusivity and exceptional cases are explained in the surrounding text.

Output field	Meaning	Value type
synonymousFractionsByPosition	Synonymous fractions by position	list of number
synonymousSiteCount	Synonymous site count	number
nonsynonymousSiteCount	Nonsynonymous site count	number

json

{
  "input": {
    "codon": "GCT"
  },
  "output": {
    "synonymousFractionsByPosition": [
      0,
      0,
      1
    ],
    "synonymousSiteCount": 1,
    "nonsynonymousSiteCount": 2
  }
}

Limitations and assumptions

A stop input is rejected. Stop-producing alternatives are nonsynonymous, and mutation biases or alternative codes are excluded.

The tool evaluates supplied observations or a declared model. It does not establish the biological cause of an observed pattern. Malformed requests produce input errors. A successfully evaluated request can still contain false flags, empty result lists or a result outside the supplied threshold; those outcomes have the meanings stated above.

Alternative or Complementary methods

Choose Kaks Selection Screen for this operation: Screen a Ka/Ks ratio relative to a caller-defined neutral band without claiming statistical significance. For a complementary task, use Premature Stop Position for this operation: Check a codon replacement for a new premature stop under the standard genetic code.

Further background: The genetic codes.

References

The genetic codes — NCBI
Synonymous Codon Sites — tool.io

Similar or alternative tools

Kaks Selection Screen
Screen a Ka/Ks ratio relative to a caller-defined neutral band without claiming statistical significance.
Premature Stop Position
Check a codon replacement for a new premature stop under the standard genetic code.