Motif Cluster
Count motif clusters using a maximum spacing.
Description
Adjacent short gaps define chained motif-position clusters.
Adjacent short gaps define chained motif-position clusters.1
Count motif clusters using a maximum spacing.
When to use Motif Cluster
Use this tool to count motif clusters using a maximum spacing.
Prepare the already measured signals, counts, coordinates, fitted coefficients or sequence strings requested. Keep assay definitions, units, aligned lists and caller-selected thresholds consistent.
How to use Motif Cluster and understand its results
- Prepare the already measured signals, counts, coordinates, fitted coefficients or sequence strings requested. Keep assay definitions, units, aligned lists and caller-selected thresholds consistent.
- Enter motifPositionsBp, maximumGapBp, minimumClusterSize using the field table and calculation rules, then run the tool.
- Read clusterCount, largestClusterSize. 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 |
|---|---|---|---|
| motifPositionsBp | Motif positions | list of number | Required |
| maximumGapBp | Maximum cluster gap | number; minimum: 0 | Required |
| minimumClusterSize | Minimum cluster size | integer; minimum: 1 | Required |
Enter nonempty finite positions, nonnegative gap and positive integer cluster-size minimum. Sort, form clusters and return qualifying count/largest size, zero if none.
join when sorted adjacent gap≤maximum Units, indexing, boundary conditions and exceptional cases are defined in the calculation rules above.
| Output field | Meaning | Value type |
|---|---|---|
| clusterCount | Cluster count | integer; minimum: 0 |
| largestClusterSize | Largest cluster size | integer; minimum: 0 |
{
"input": {
"motifPositionsBp": [
10,
20,
100,
105,
110
],
"maximumGapBp": 15,
"minimumClusterSize": 2
},
"output": {
"clusterCount": 2,
"largestClusterSize": 3
}
}Limitations and assumptions
Duplicates count separately. No motif search, chromosome grouping or total-span ceiling is supplied.
Numeric inputs, where present, must be finite. Follow the calculation-specific rules for overflow, underflow and exceptional cases. Lists are limited to 100,000 entries; the rules above may require smaller limits. Missing required fields, extra fields, wrong value types and violations of the calculation rules are input errors.
Alternative or Complementary methods
Use TAD Boundary Distance: Measure adjacent TAD boundary distances. For a complementary task, use CRISPR Off-Target Count: Count CRISPR epigenome-editing off-targets by mismatch risk threshold.
References
-
Motif Cluster — tool.io
Similar or alternative tools
- TAD Boundary Distance
Measure adjacent TAD boundary distances.
- CRISPR Off-Target Count
Count CRISPR epigenome-editing off-targets by mismatch risk threshold.