Start-Stop Codon Distance bp ORF Length Calculator
Compute ORF length from independently identified same-frame zero-based codon starts, excluding the stop from translated length; no ORF scan.
Description
Compute ORF length from independently identified same-frame zero-based codon starts, excluding the stop from translated length; no ORF scan.
An open-reading-frame length calculation needs consistent codon-start offsets. Including the stop codon in a span differs from counting amino-acid-coding bases.
When to use this tool
Compute ORF length from independently identified same-frame zero-based codon starts, excluding the stop from translated length; no ORF scan.
- Prepare the supplied startCodonOffset, stopCodonOffset 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 startCodonOffset, stopCodonOffset. 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.codingBasesExcludingStop, result.aminoAcidCount, result.spanIncludingStop. Interpret false, null and empty lists using the distinctions below; they can be valid outputs.
Require nonnegative integer startCodonOffset and stopCodonOffset at least three bases later. Reject a difference not divisible by three. Return that difference as codingBasesExcludingStop, divide by three for aminoAcidCount, and add three for spanIncludingStop.1
| Input field | Meaning and representation | Accepted input |
|---|---|---|
| startCodonOffset | start codon offset. | Integer from 0 to 1e12 inclusive |
| stopCodonOffset | stop codon offset. | Integer from startCodonOffset + 3 to 1e12 inclusive |
| Output field | Interpretation |
|---|---|
| result | Object containing the named outputs below. |
| result.codingBasesExcludingStop | The coding bases excluding stop value under the stated formula or text convention. |
| result.aminoAcidCount | The amino acid count value under the stated formula or text convention. |
| result.spanIncludingStop | The span including stop value under the stated formula or text convention. |
{
"input": {
"startCodonOffset": 0,
"stopCodonOffset": 9
},
"output": {
"result": {
"codingBasesExcludingStop": 9,
"aminoAcidCount": 3,
"spanIncludingStop": 12
}
}
}Limitations and assumptions
- Offsets are zero-based codon starts in the same forward coordinate frame. The tool does not scan codons, model introns or alternate reading frames, or validate sequence translation.
- 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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