Description
Check stop-symbol placement under a supplied terminal policy.
Sequence text, ambiguity codes and encoded quality scores describe different information. Literal alphabets and Phred transformations can be checked without identifying a molecule or proving calibrated sequencing accuracy; missingness and reporting encodings require explicit conventions.
Check stop-symbol placement under a supplied terminal policy.
When to use this tool
Use Protein Stop Symbol Terminal Policy when checking the stated sequence token, ambiguity, quality symbol or local trimming convention.
How to use the tool and how it works
- Enter sequence, allowTerminal. Use the units and conventions below.
- Run the tool. Correct any format, range, or cross-field input error before interpreting the output.
- Read valid, terminalStop, internalStop. Inspect valid, terminalStop, internalStop before interpreting the associated values.
Check stop-symbol placement under a supplied terminal policy. Accept uppercase ASCII letters and asterisks, including empty text; detect final asterisk and any earlier asterisk, valid excludes internal stops and disallowed terminal stops.1
| Input field | Meaning and units | Accepted input |
|---|---|---|
| sequence | Sequence | Required. Text; maximum UTF-16 length 8192. |
| allowTerminal | Allow Terminal | Required. Boolean. |
| Output field | Interpretation | Returned shape |
|---|---|---|
| valid | Whether this local input/result condition holds; inspect the limitations before treating it as full validation. | Required. Boolean. |
| terminalStop | Terminal Stop | Required. Boolean. |
| internalStop | Internal Stop | Required. Boolean. |
{
"input": {
"sequence": "MPEP*",
"allowTerminal": true
},
"output": {
"valid": true,
"terminalStop": true,
"internalStop": false
}
}Limitations and assumptions
- The alphabet admits letters beyond a canonical amino-acid set; no translation, genetic code or biological protein validity is inferred.
- Inputs must satisfy both the field types and the cross-field conditions above. Invalid input causes an error; a successful false flag or documented placeholder is a different result.
Alternative or Complementary methods
Use a complete format-aware sequence/quality workflow and the appropriate reference/genetic code; assess biological identity and quality calibration independently.
References
Similar or alternative tools
- Codon Degeneracy Supplied Code Record
Count codons for one residue under a supplied code table.
- Protein Residue Position Label
Label an explicitly supplied protein residue symbol and one-based position without checking a sequence or inferring a substitution.