Polyalanine Consecutive A Run Length Finder
Find the longest consecutive A run with tied zero-based start offsets in canonical protein sequence; no disease threshold.
Description
Find the longest consecutive A run with tied zero-based start offsets in canonical protein sequence; no disease threshold.
A homopolymeric alanine tract is a consecutive run rather than a total alanine count. Reporting tied starts distinguishes several equally long tracts.
When to use this tool
Find the longest consecutive A run with tied zero-based start offsets in canonical protein sequence; no disease threshold.
- Prepare the supplied sequence 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 sequence. 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.longestRun, result.tiedStartOffsets. Interpret false, null and empty lists using the distinctions below; they can be valid outputs.
Normalize and validate the protein sequence, scan consecutive A residues, and track the longest run length with all zero-based starts tying that length. Return zero and an empty start list when none occur.1
| Input field | Meaning and representation | Accepted input |
|---|---|---|
| sequence | 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.longestRun | The longest run value under the stated formula or text convention. |
| result.tiedStartOffsets | The tied start offsets list in the ordering and representation described above. |
{
"input": {
"sequence": "AAAGAAA"
},
"output": {
"result": {
"longestRun": 3,
"tiedStartOffsets": [
0,
4
]
}
}
}Limitations and assumptions
- Offsets refer to the uppercased sequence after trimming its ends; internal whitespace is rejected. This does not assess function, disease relevance or sequence alignment; only contiguous exact A runs are counted.
- Protein inputs are trimmed at their ends and uppercased; internal whitespace is not removed. Only the twenty canonical amino-acid letters are accepted, with no FASTA header, ambiguity code or stop symbol.
- 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
Use compatible mass, charge and sequence conventions when combining these operations. Inspect experimental spectra or quantitative controls separately; sequence features and theoretical mass arithmetic are not peptide identification or biological interpretation.
References
Similar or alternative tools
- Polyglutamine Consecutive Q Run Length Finder
Find the longest consecutive Q run with tied zero-based start offsets in canonical protein sequence; no disease threshold.
- digest length filter
Digest length filtering selects supplied peptide strings by an inclusive length range.