Nucleosome Positioning
Classify nucleosome positioning from center dispersion.
Description
Center-position dispersion summarizes consistency under a chosen spread criterion.
Center-position dispersion summarizes consistency under a chosen spread criterion.1
Classify nucleosome positioning from center dispersion.
When to use Nucleosome Positioning
Use this tool to classify nucleosome positioning from center dispersion.
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 Nucleosome Positioning 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 centerPositionsBp, maximumStdDevBp using the field table and calculation rules, then run the tool.
- Read meanCenterBp, positionStdDevBp, call. 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 |
|---|---|---|---|
| centerPositionsBp | Nucleosome centers | list of number | Required |
| maximumStdDevBp | Maximum standard deviation | number; minimum: 0 | Required |
Enter nonempty finite centers and nonnegative maximum. Return mean, population SD and well-positioned/fuzzy label. One center gives zero SD.
SD=sqrt(mean((center−mean)²)); pass=SD≤maximum Units, indexing, boundary conditions and exceptional cases are defined in the calculation rules above.
| Output field | Meaning | Value type |
|---|---|---|
| meanCenterBp | Mean center | number |
| positionStdDevBp | Position standard deviation | number; minimum: 0 |
| call | Positioning call | string; one of "well-positioned", "fuzzy" |
{
"input": {
"centerPositionsBp": [
99,
100,
101
],
"maximumStdDevBp": 1
},
"output": {
"meanCenterBp": 100,
"positionStdDevBp": 0.816496580927726,
"call": "well-positioned"
}
}Limitations and assumptions
No nucleosome detection or universal biological classification 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 Nucleosome Repeat Length: Estimate nucleosome repeat length from ordered periodicity peaks. For a complementary task, use Linker DNA Length: Derive linker DNA length from repeat and core-particle lengths.
References
-
Nucleosome Positioning — tool.io
Similar or alternative tools
- Nucleosome Repeat Length
Estimate nucleosome repeat length from ordered periodicity peaks.
- Linker DNA Length
Derive linker DNA length from repeat and core-particle lengths.