Nucleosome Repeat Length
Estimate nucleosome repeat length from ordered periodicity peaks.
Description
Nucleosome repeat spacing is the distance between consecutive supplied centers.
Nucleosome repeat spacing is the distance between consecutive supplied centers.1
Estimate nucleosome repeat length from ordered periodicity peaks.
When to use Nucleosome Repeat Length
Use this tool to estimate nucleosome repeat length from ordered periodicity peaks.
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 Repeat Length 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 peakPositionsBp using the field table and calculation rules, then run the tool.
- Read meanRepeatLengthBp, minimumSpacingBp, maximumSpacingBp, spacingStdDevBp. 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 |
|---|---|---|---|
| peakPositionsBp | Nucleosome peak positions (bp) | list of number | Required |
Enter at least two strictly increasing finite positions. Compute adjacent spacings, then return their mean, extrema and population SD.
spacing=next−previous; SD=sqrt(mean((spacing−mean)²)) Units, indexing, boundary conditions and exceptional cases are defined in the calculation rules above.
| Output field | Meaning | Value type |
|---|---|---|
| meanRepeatLengthBp | Mean repeat length (bp) | number; minimum: 0 |
| minimumSpacingBp | Minimum peak spacing (bp) | number; minimum: 0 |
| maximumSpacingBp | Maximum peak spacing (bp) | number; minimum: 0 |
| spacingStdDevBp | Spacing standard deviation (bp) | number; minimum: 0 |
{
"input": {
"peakPositionsBp": [
0,
200,
410
]
},
"output": {
"meanRepeatLengthBp": 205,
"minimumSpacingBp": 200,
"maximumSpacingBp": 210,
"spacingStdDevBp": 5
}
}Limitations and assumptions
Signed/fractional positions are accepted. No nucleosome peaks are detected.
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 Linker DNA Length: Derive linker DNA length from repeat and core-particle lengths. For a complementary task, use Nucleosome Positioning: Classify nucleosome positioning from center dispersion.
References
-
Nucleosome Repeat Length — tool.io
Similar or alternative tools
- Linker DNA Length
Derive linker DNA length from repeat and core-particle lengths.
- Nucleosome Positioning
Classify nucleosome positioning from center dispersion.