Operator Repressor Binding Motif Palindrome Half-Site Checker
Check a full reverse-complement palindrome and report half-sites; sequence symmetry alone does not prove operator/repressor binding.
Description
Check a full reverse-complement palindrome and report half-sites; sequence symmetry alone does not prove operator/repressor binding.
A DNA reverse-complement palindrome has the same sequence when reversed and base-complemented. Such symmetry is a sequence property, separate from evidence of protein binding.
When to use this tool
Check a full reverse-complement palindrome and report half-sites; sequence symmetry alone does not prove operator/repressor binding.
- Prepare the supplied dnaSequence 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 dnaSequence. 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.reverseComplementPalindrome, result.leftHalf, result.rightHalf, result.repressorBindingEstablished. Interpret false, null and empty lists using the distinctions below; they can be valid outputs.
Uppercase dnaSequence, require nonempty even-length text containing only A/C/G/T, construct its reverse complement, and compare for exact equality. Return both halves and repressorBindingEstablished false.1
| Input field | Meaning and representation | Accepted input |
|---|---|---|
| dnaSequence | dna sequence. | Text; at most 8,192 UTF-16 code units, subject to the grammar above |
| Output field | Interpretation |
|---|---|
| result | Object containing the named outputs below. |
| result.reverseComplementPalindrome | Flag for reverse complement palindrome under the exact condition described above. |
| result.leftHalf | The left half value under the stated formula or text convention. |
| result.rightHalf | The right half value under the stated formula or text convention. |
| result.repressorBindingEstablished | Flag for repressor binding established under the exact condition described above. |
{
"input": {
"dnaSequence": "GAATTC"
},
"output": {
"result": {
"reverseComplementPalindrome": true,
"leftHalf": "GAA",
"rightHalf": "TTC",
"repressorBindingEstablished": false
}
}
}Limitations and assumptions
- Whitespace and ambiguous bases are rejected rather than stripped. The tool does not search internal motifs, score approximate symmetry or establish an operator's biological activity.
- 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
Keep model assumptions and phenotype-category order with each result. Ratio tolerance screens differ from goodness-of-fit inference, and sequence matches or likelihood products do not independently establish a biological mechanism or personal identity.
References
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