Description
Count codons for one residue under a supplied code table.
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.
Count codons for one residue under a supplied code table.
When to use this tool
Use Codon Degeneracy Supplied Code Record when checking the stated sequence token, ambiguity, quality symbol or local trimming convention.
How to use the tool and how it works
- Enter codons, residues, residue. Follow any array-alignment requirements below. Use the units and conventions below.
- Run the tool. Correct any format, range, or cross-field input error before interpreting the output.
- Read synonymousCodons, degeneracy. Use the output convention below.
Count codons for one residue under a supplied code table. Require aligned residues/codons, unique uppercase A/C/G/T triplets; synonymousCodons selects matching residue labels, degeneracy is their count.1
| Input field | Meaning and units | Accepted input |
|---|---|---|
| codons | Codons | Required. Array of text; maximum UTF-16 length 8192; maximum items 256. |
| residues | Residues | Required. Array of text; maximum UTF-16 length 8192; maximum items 256. |
| residue | Residue | Required. Text; maximum UTF-16 length 8192. |
| Output field | Interpretation | Returned shape |
|---|---|---|
| synonymousCodons | Synonymous Codons | Required. Array of text; maximum UTF-16 length 8192; maximum items 256. |
| degeneracy | Degeneracy | Required. Safe integer. |
{
"input": {
"codons": [
"AAA",
"AAG",
"AAC"
],
"residues": [
"K",
"K",
"N"
],
"residue": "K"
},
"output": {
"synonymousCodons": [
"AAA",
"AAG"
],
"degeneracy": 2
}
}Limitations and assumptions
- The code may be partial and residue labels are literal; no standard genetic code is selected or verified.
- 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
- Protein Stop Symbol Terminal Policy
Check stop-symbol placement under a supplied terminal policy.
- Codon Start Stop Source Tag
Record an explicit codon role and genetic-code source without assigning start or stop status across code tables.