Tandem Repeat Count
Find the longest consecutive tandem repeat of a supplied peptide motif.
Description
Tandem repeats consist of consecutive copies of a supplied motif.
Tandem repeats consist of consecutive copies of a supplied motif. The longest-run search examines every possible starting residue.1
Find the longest consecutive tandem repeat of a supplied peptide motif.
When to use Tandem Repeat Count
Use this tool to find the longest consecutive tandem repeat of a supplied peptide motif.
Prepare the canonical sequence, peptide assignments, fitted assay parameters or upstream measurements requested. Keep corresponding entries aligned, use the stated mass and signal units, and remove FASTA headers before entering sequence text.
How to use Tandem Repeat Count and understand its results
- Prepare the canonical sequence, peptide assignments, fitted assay parameters or upstream measurements requested. Keep corresponding entries aligned, use the stated mass and signal units, and remove FASTA headers before entering sequence text.
- Enter sequence, motif using the field table and calculation rules, then run the tool.
- Read longestTandemRun, runStart. The explanation below defines the units, signs, ordering and any flags or placeholder values.
- If the tool reports an input issue, correct the values and run it again. Apply the stated assumptions when interpreting a successfully returned result.
| Input field | Meaning | Value type; see rules below | Requirement |
|---|---|---|---|
| sequence | Sequence | string | Required |
| motif | Motif | string | Required |
Enter canonical sequence and nonempty canonical motif. Return longest copy count and zero-based run start. Ties retain the earliest start; no match returns count zero and start −1.
The shared sequence helper trims outer whitespace and uppercases the sequence. It requires at least one residue from ACDEFGHIKLMNPQRSTVWY. Internal whitespace, FASTA headers, ambiguous letters and modified-residue notation are rejected. Sequence indexes refer to the normalized sequence; individual tools may preserve original strings in their returned lists as explained above.
longestRun=max_i consecutive exact motif copies starting at i Units, indexing, boundary conditions and exceptional cases are defined in the calculation rules above.
| Output field | Meaning | Value type |
|---|---|---|
| longestTandemRun | Longest tandem run | number |
| runStart | Run start | number |
{
"input": {
"sequence": "ACACAC",
"motif": "AC"
},
"output": {
"longestTandemRun": 3,
"runStart": 0
}
}Limitations and assumptions
The scan uses exact ungapped sequence matches and does not score substitutions, interrupted repeats or repeat function.
Numeric inputs must be finite. Follow the calculation-specific rules for overflow, underflow and exceptional cases. Extremely large text inputs are rejected. Missing required fields, extra fields, wrong value types and violations of the calculation rules are input errors.
Alternative or Complementary methods
Use Low Complexity Windows: Detect compositionally biased low-complexity windows. For a complementary task, use Leucine Zipper Pattern: Scan every seventh residue for leucine-zipper runs.
References
-
Tandem Repeat Count — tool.io
Similar or alternative tools
- Low Complexity Windows
Detect compositionally biased low-complexity windows.
- Leucine Zipper Pattern
Scan every seventh residue for leucine-zipper runs.