Ribosome Binding Spacing

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

Description

A bacterial ribosome-binding motif can support translation initiation when located before a start codon at a suitable spacing.

A bacterial ribosome-binding motif can support translation initiation when located before a start codon at a suitable spacing. Motif presence alone is not expression evidence.

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

When to use Ribosome Binding Spacing

Use this for the following task: Locate AGGAGG ribosome-binding motifs at compatible spacing before a specified ATG start.

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

How to use Ribosome Binding Spacing 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, minimumSpacingBp, maximumSpacingBp using the field table, then run the tool.
Read bindingSiteStarts, spacingsBp, supportedSites. 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
minimumSpacingBp	Minimum spacing bp	integer	Required
maximumSpacingBp	Maximum spacing bp	integer	Required

Normalize canonical DNA and require an ATG at the supplied zero-based start. Scan exact AGGAGG matches ending before it and retain gaps inside inclusive supplied bounds.^[1]

gap = ATGstart − (AGGAGGstart+6)

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

Output field	Meaning	Value type
bindingSiteStarts	Binding site starts	list of number
spacingsBp	Spacings bp	list of number
supportedSites	Supported sites	number

json

{
  "input": {
    "sequence": "AGGAGGAAAAATG",
    "startCodonIndex": 10,
    "minimumSpacingBp": 3,
    "maximumSpacingBp": 8
  },
  "output": {
    "bindingSiteStarts": [
      0
    ],
    "spacingsBp": [
      4
    ],
    "supportedSites": 1
  }
}

Limitations and assumptions

Alternative motifs and start codons are excluded. The tool does not model RNA structure or translation efficiency.

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 Kozak Start Context for this operation: Rate Kozak context from the minus-three purine and plus-four G surrounding a specified ATG. For a complementary task, use Bacterial Promoter Spacing for this operation: Check the inter-box gap between supplied bacterial minus-35 and minus-10 promoter motifs.

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

References

Ribosome Binding Spacing — tool.io

Similar or alternative tools

Kozak Start Context
Rate Kozak context from the minus-three purine and plus-four G surrounding a specified ATG.
Bacterial Promoter Spacing
Check the inter-box gap between supplied bacterial minus-35 and minus-10 promoter motifs.