Low Complexity Region Fraction
Union long low-complexity stretches and calculate their protein coverage.
Description
Low-complexity-region coverage unions supplied intervals after filtering each by its own length.
Low-complexity-region coverage unions supplied intervals after filtering each by its own length. Overlapping retained intervals contribute each position only once.1
Union long low-complexity stretches and calculate their protein coverage.
When to use Low Complexity Region Fraction
Use this tool to union long low-complexity stretches and calculate their protein coverage.
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 Low Complexity Region Fraction 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 sequenceLength, regionStarts, regionEnds, minimumStretch using the field table and calculation rules, then run the tool.
- Read longRegionCount, coveredResidues, lowComplexityFraction. 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 |
|---|---|---|---|
| sequenceLength | Sequence length | number | Required |
| regionStarts | Region starts | list of number | Required |
| regionEnds | Region ends | list of number | Required |
| minimumStretch | Minimum stretch | number | Required |
Enter positive safe-integer sequence length, aligned valid zero-based half-open intervals and positive safe-integer stretch minimum. Empty interval lists are allowed. Return retained interval count, covered residues and coverage fraction.
retain if end−start≥minimumStretch; fraction=size(union retained intervals)/sequenceLength Units, indexing, boundary conditions and exceptional cases are defined in the calculation rules above.
| Output field | Meaning | Value type |
|---|---|---|
| longRegionCount | Long region count | number |
| coveredResidues | Covered residues | number |
| lowComplexityFraction | Low complexity fraction | number |
{
"input": {
"sequenceLength": 10,
"regionStarts": [
0,
5
],
"regionEnds": [
3,
9
],
"minimumStretch": 3
},
"output": {
"longRegionCount": 2,
"coveredResidues": 7,
"lowComplexityFraction": 0.7
}
}Limitations and assumptions
The count is retained input intervals, not merged region count. No sequence classification is performed; long coverage spans enumerate positions individually.
Numeric inputs 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 Low Complexity Windows: Detect compositionally biased low-complexity windows. For a complementary task, use Protein Sequence Coverage: Measure protein sequence coverage as the union of peptide intervals.
References
-
Low Complexity Region Fraction — tool.io
Similar or alternative tools
- Low Complexity Windows
Detect compositionally biased low-complexity windows.
- Protein Sequence Coverage
Measure protein sequence coverage as the union of peptide intervals.