Plastid IR Inverted Repeat Contraction Expansion Event Note Generator
Record IR length change from independently homologized plastid boundaries; does not establish evolutionary event homology.
Description
Record IR length change from independently homologized plastid boundaries; does not establish evolutionary event homology.
An inverted-repeat length change can be labeled expansion or contraction before its biological cause is investigated. Comparing lengths alone is simpler than establishing homologous boundary changes.
When to use this tool
Record IR length change from independently homologized plastid boundaries; does not establish evolutionary event homology.
- Prepare the supplied beforeIrLengthBp, afterIrLengthBp fields for this operation.
- Compare the complete example with the representation used by your own input before carrying the result into another step.
How to use the tool and how it works
- Enter beforeIrLengthBp, afterIrLengthBp. Use the exact text syntax, units and index conventions explained below.
- Run the tool. If input validation fails, correct the supplied fields before interpreting any result.
- Read result.signedLengthChangeBp, result.event, result.homologyEstablished. Interpret false, null and empty lists using the distinctions below; they can be valid outputs.
Validate nonnegative bounded integer beforeIrLengthBp/afterIrLengthBp. Subtract before from after, label the sign as expansion, contraction or unchanged, and set homologyEstablished false.1
| Input field | Meaning and representation | Accepted input |
|---|---|---|
| beforeIrLengthBp | before ir length bp. | Integer from 0 to 1e9 inclusive |
| afterIrLengthBp | after ir length bp. | Integer from 0 to 1e9 inclusive |
| Output field | Interpretation |
|---|---|
| result | Object containing the named outputs below. |
| result.signedLengthChangeBp | The signed length change bp value under the stated formula or text convention. |
| result.event | The event value under the stated formula or text convention. |
| result.homologyEstablished | Flag for homology established under the exact condition described above. |
{
"input": {
"beforeIrLengthBp": 100,
"afterIrLengthBp": 120
},
"output": {
"result": {
"signedLengthChangeBp": 20,
"event": "expansion",
"homologyEstablished": false
}
}
}Limitations and assumptions
- The tool does not align sequences or confirm that both measurements describe the same homologous repeat. Breakpoints, assembly quality and sequence variation are not evaluated.
- Every declared top-level field is required and unexpected fields are rejected. Numeric inputs must be finite; ordinary text fields are bounded to 8,192 UTF-16 code units, with tighter operation-specific limits where stated.
- Ordinary string lists have at most 128 entries of at most 128 code units each; numeric lists and matrices have separate bounded size checks. Nonfinite results and excessively large serialized outputs are rejected.
- Indexes are zero-based and spans have an exclusive end unless explicitly stated otherwise. A valid false, null or empty-list result is distinct from malformed input.
Alternative or Complementary methods
Retain the reference assembly, accession/version and measurement convention with an analysis. Length summaries, flags and lookup notes do not validate an assembly or classify a variant; use the corresponding sequence, alignment or evidence-review workflow.
References
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