Description
Return ambiguous positions in an IUPAC DNA codon.
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.
Return ambiguous positions in an IUPAC DNA codon.
When to use this tool
Use Bioinformatics: Codon Ambiguity Position Mask when checking the stated sequence token, ambiguity, quality symbol or local trimming convention.
How to use the tool and how it works
- Enter codon. Use the units and conventions below.
- Run the tool. Correct any format, range, or cross-field input error before interpreting the output.
- Read result. Expand result to inspect the returned fields.
Return ambiguous positions in an IUPAC DNA codon. Require exactly three uppercase supported DNA symbols; ambiguousPositions uses one-based positions for non-A/C/G/T symbols, unambiguous requires only those four bases.1
| Input field | Meaning and units | Accepted input |
|---|---|---|
| codon | Codon | Required. Text. Implementation limit: 8192 Unicode code points and 16384 UTF-16 code units. |
| Output field | Interpretation | Returned shape |
|---|---|---|
| result | Returned calculated value or nested object under the stated output convention. | Required. Object. |
| result.ambiguousPositions | One-based codon positions containing an allowed non-A/C/G/T ambiguity symbol. | Calculated result member: array. |
| result.unambiguous | Unambiguous | Calculated result member: boolean. |
{
"input": {
"codon": "ARN"
},
"output": {
"result": {
"ambiguousPositions": [
2,
3
],
"unambiguous": false
}
}
}Limitations and assumptions
- Positions are one-based, unlike several neighboring helpers; no translation or ambiguity probability is computed.
- Outputs are nested inside result. 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
- FASTA Iupac Ambiguity Cardinality
Expand one uppercase IUPAC DNA ambiguity symbol.
- Kmer Canonical Reverse Complement Pair
Return a DNA k-mer's reverse complement and canonical representative.