Kozak Start Context

Rate Kozak context from the minus-three purine and plus-four G surrounding a specified ATG.

Description

A simplified Kozak screen examines the −3 and +4 positions around an ATG start.

A simplified Kozak screen examines the −3 and +4 positions around an ATG start. A purine at −3 and G at +4 form its two criteria.

Rate Kozak context from the minus-three purine and plus-four G surrounding a specified ATG.

When to use Kozak Start Context

Use this for the following task: Rate Kozak context from the minus-three purine and plus-four G surrounding a specified ATG.

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

How to use Kozak Start Context and understand its results

Prepare the observed records or explicit model parameters requested below. Keep probabilities as fractions and paired records aligned.
Enter sequence, startCodonIndex using the field table, then run the tool.
Read minusThreeBase, plusFourBase, contextStrength. 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
sequence	Sequence	string	Required
startCodonIndex	Start codon index	integer	Required

Normalize canonical DNA and require a zero-based ATG start with both flanking positions available. Read start−3 and start+3 and classify their combination.^[1]

strength = strong if both criteria, intermediate if one, weak if none

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

Output field	Meaning	Value type
minusThreeBase	Minus three base	string
plusFourBase	Plus four base	string
contextStrength	Context strength	string

json

{
  "input": {
    "sequence": "GCCACCATGG",
    "startCodonIndex": 6
  },
  "output": {
    "minusThreeBase": "A",
    "plusFourBase": "G",
    "contextStrength": "strong"
  }
}

Limitations and assumptions

ATG’s A is position +1 in the biological convention. This does not predict translation efficiency or examine the full initiation context.

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 Ribosome Binding Spacing for this operation: Locate AGGAGG ribosome-binding motifs at compatible spacing before a specified ATG start. For a complementary task, use 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.

The implementation reference documents the exact calculation, supported input shapes and returned fields.

References

Kozak Start Context — tool.io

Similar or alternative tools

Ribosome Binding Spacing
Locate AGGAGG ribosome-binding motifs at compatible spacing before a specified ATG start.
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.