Low Complexity Windows
Detect compositionally biased low-complexity windows.
Description
A low-complexity window screen measures dominance by a single amino-acid type.
A low-complexity window screen measures dominance by a single amino-acid type. High dominance can identify compositionally biased segments.1
Detect compositionally biased low-complexity windows.
When to use Low Complexity Windows
Use this tool to detect compositionally biased low-complexity windows.
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 Windows 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, windowLength, minimumDominantFraction using the field table and calculation rules, then run the tool.
- Read lowComplexityStarts, maximumDominantFraction. 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 |
| windowLength | Window length | number | Required |
| minimumDominantFraction | Minimum dominant fraction | number | Required |
Enter a canonical sequence, safe-integer window within its length and minimum fraction in 0–1. Slide by one residue; return qualifying zero-based starts and maximum dominant fraction, including threshold equality.
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.
dominantFraction_i=max(residue counts in window_i)/windowLength Units, indexing, boundary conditions and exceptional cases are defined in the calculation rules above.
| Output field | Meaning | Value type |
|---|---|---|
| lowComplexityStarts | Low complexity starts | list of number |
| maximumDominantFraction | Maximum dominant fraction | number |
{
"input": {
"sequence": "AAAAFG",
"windowLength": 4,
"minimumDominantFraction": 0.75
},
"output": {
"lowComplexityStarts": [
0,
1
],
"maximumDominantFraction": 1
}
}Limitations and assumptions
This is not an entropy-based or multiresidue low-complexity classifier. Overlapping windows are not merged, and large windows make its repeated counting expensive.
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 Region Fraction: Union long low-complexity stretches and calculate their protein coverage. For a complementary task, use Tandem Repeat Count: Find the longest consecutive tandem repeat of a supplied peptide motif.
References
-
Low Complexity Windows — tool.io
Similar or alternative tools
- Low Complexity Region Fraction
Union long low-complexity stretches and calculate their protein coverage.
- Tandem Repeat Count
Find the longest consecutive tandem repeat of a supplied peptide motif.