Operon Coding Interval Audit
Audit coding intervals in one bacterial transcript and count its cistrons.
Description
A bacterial transcript can contain multiple coding regions or cistrons.
A bacterial transcript can contain multiple coding regions or cistrons. Interval auditing checks their ordered placement within a supplied transcript extent.
Audit coding intervals in one bacterial transcript and count its cistrons.
When to use Operon Coding Interval Audit
Use this for the following task: Audit coding intervals in one bacterial transcript and count its cistrons.
Prepare the observed records or explicit model parameters requested below. Keep probabilities as fractions and paired records aligned.
How to use Operon Coding Interval Audit and understand its results
- Prepare the observed records or explicit model parameters requested below. Keep probabilities as fractions and paired records aligned.
- Enter orfStarts, orfEnds, transcriptEnd using the field table, then run the tool.
- Read orfCount, polycistronic, codingBases. 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 |
|---|---|---|---|
| orfStarts | Orf starts | list of number; each entry: number | Required |
| orfEnds | Orf ends | list of number; each entry: number | Required |
| transcriptEnd | Transcript end | integer | Required |
Supply aligned ordered nonoverlapping positive-length half-open ORF intervals contained within transcriptEnd. Count regions and sum their lengths.1
codingBases = Σ(orfEnd−orfStart); polycistronic = orfCount > 1 This summarizes the declared operation. Units, indexing, inclusivity and exceptional cases are explained in the surrounding text.
| Output field | Meaning | Value type |
|---|---|---|
| orfCount | Orf count | number |
| polycistronic | Polycistronic | boolean |
| codingBases | Coding bases | number |
{
"input": {
"orfStarts": [
0,
10,
20
],
"orfEnds": [
6,
16,
26
],
"transcriptEnd": 30
},
"output": {
"orfCount": 3,
"polycistronic": true,
"codingBases": 18
}
}Limitations and assumptions
Touching intervals are accepted. The tool does not identify ORFs, promoter boundaries or translated products.
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 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
-
Operon Coding Interval Audit — tool.io
Similar or alternative tools
- Ribosome Binding Spacing
Locate AGGAGG ribosome-binding motifs at compatible spacing before a specified ATG start.
- Bacterial Promoter Spacing
Check the inter-box gap between supplied bacterial minus-35 and minus-10 promoter motifs.