Transmembrane Window Scan
Detect transmembrane helix candidates from local hydropathy windows.
Description
A local hydropathy scan finds sequence windows meeting a chosen mean score.
A local hydropathy scan finds sequence windows meeting a chosen mean score. High hydropathy is a candidate feature rather than proof of a transmembrane helix.1
Detect transmembrane helix candidates from local hydropathy windows.
When to use Transmembrane Window Scan
Use this tool to detect transmembrane helix candidates from local hydropathy 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 Transmembrane Window Scan 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, minimumMeanHydropathy using the field table and calculation rules, then run the tool.
- Read candidateStarts, maximumMeanHydropathy. 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 |
| minimumMeanHydropathy | Minimum mean hydropathy | number | Required |
Enter a canonical sequence, a safe-integer window from one through sequence length and any finite minimum score. Slide by one residue and return zero-based qualifying starts and the maximum mean.
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.
mean_i=ΣKyte–Doolittle(window_i)/windowLength; candidate if mean_i≥minimum Units, indexing, boundary conditions and exceptional cases are defined in the calculation rules above.
| Output field | Meaning | Value type |
|---|---|---|
| candidateStarts | Candidate starts | list of number |
| maximumMeanHydropathy | Maximum mean hydropathy | number |
{
"input": {
"sequence": "AAAAAAA",
"windowLength": 4,
"minimumMeanHydropathy": 1.5
},
"output": {
"candidateStarts": [
0,
1,
2,
3
],
"maximumMeanHydropathy": 1.8
}
}Limitations and assumptions
Overlapping windows are not merged. Membrane topology, signal peptides and a calibrated classifier are not modeled.
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 Signal Peptide Core Scan: Summarize N-region charge and hydrophobic signal-peptide core. For a complementary task, use Protein GRAVY: Compute grand average of Kyte–Doolittle hydropathy.
References
-
Transmembrane Window Scan — tool.io
Similar or alternative tools
- Signal Peptide Core Scan
Summarize N-region charge and hydrophobic signal-peptide core.
- Protein GRAVY
Compute grand average of Kyte–Doolittle hydropathy.