Premature Stop Position

Check a codon replacement for a new premature stop under the standard genetic code.

Description

A codon replacement can introduce a stop earlier than the original translated sequence.

A codon replacement can introduce a stop earlier than the original translated sequence. The relevant length is the number of amino acids before the first in-frame stop.^[1]

Check a codon replacement for a new premature stop under the standard genetic code.

When to use Premature Stop Position

Use this for the following task: Check a codon replacement for a new premature stop under the standard genetic code.

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

How to use Premature Stop Position and understand its results

Prepare the observed records or explicit model parameters requested below. Keep probabilities as fractions and paired records aligned.
Enter codingSequence, mutatedCodonIndex, mutatedCodon using the field table, then run the tool.
Read originalAminoAcid, replacementAminoAcid, prematureStop, retainedAminoAcids. 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
codingSequence	Coding sequence	string	Required
mutatedCodonIndex	Mutated codon index	integer	Required
mutatedCodon	Mutated codon	string	Required

Use an in-frame canonical coding sequence, zero-based codon index and replacement triplet. Translate with the standard code, replace that codon and compare first-stop positions.^[2]

prematureStop = replacement is stop AND new first-stop index < original first-stop index

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

Output field	Meaning	Value type
originalAminoAcid	Original amino acid	string
replacementAminoAcid	Replacement amino acid	string
prematureStop	Premature stop	boolean
retainedAminoAcids	Retained amino acids	number

json

{
  "input": {
    "codingSequence": "ATGAAATAA",
    "mutatedCodonIndex": 1,
    "mutatedCodon": "TAG"
  },
  "output": {
    "originalAminoAcid": "K",
    "replacementAminoAcid": "*",
    "prematureStop": true,
    "retainedAminoAcids": 1
  }
}

Limitations and assumptions

Retained amino acids exclude the stop. This does not model splicing, nonsense-mediated decay or pathogenicity.

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 Coding Frame Integrity for this operation: Screen an in-frame canonical DNA coding sequence using the standard ATG start and TAA/TAG/TGA stops, with chosen start/terminal-stop requirements. For a complementary task, use Synonymous Codon Sites for this operation: Count equally weighted synonymous single-base alternatives by codon position using the standard code.

Further background: The genetic codes.

References

The genetic codes — NCBI
Premature Stop Position — tool.io

Similar or alternative tools

Coding Frame Integrity
Screen an in-frame canonical DNA coding sequence using the standard ATG start and TAA/TAG/TGA stops, with chosen start/terminal-stop requirements.
Synonymous Codon Sites
Count equally weighted synonymous single-base alternatives by codon position using the standard code.