Signal Peptide Core Scan

Summarize N-region charge and hydrophobic signal-peptide core.

Description

A signal-peptide screen combines a basic residue in an initial segment with a hydrophobic segment immediately after it.

A signal-peptide screen combines a basic residue in an initial segment with a hydrophobic segment immediately after it. The selected segment lengths determine what is tested.^[1]

Summarize N-region charge and hydrophobic signal-peptide core.

When to use Signal Peptide Core Scan

Use this tool to summarize N-region charge and hydrophobic signal-peptide core.

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 Signal Peptide Core 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, nRegionLength, coreWindowLength, minimumCoreHydropathy using the field table and calculation rules, then run the tool.
Read coreStart, coreMeanHydropathy, positiveNRegion, candidate. 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
nRegionLength	N region length	number	Required
coreWindowLength	Core window length	number	Required
minimumCoreHydropathy	Minimum core hydropathy	number	Required

Enter positive safe-integer N-region and core lengths that fit within the canonical sequence and a finite minimum hydropathy. Inspect that fixed adjacent core rather than searching for the best window; return zero-based core start, mean score and flags.

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.

candidate=(N-region contains K/R) AND (coreMeanHydropathy≥minimum)

Units, indexing, boundary conditions and exceptional cases are defined in the calculation rules above.

Output field	Meaning	Value type
coreStart	Core start	number
coreMeanHydropathy	Core mean hydropathy	number
positiveNRegion	Positive n region	boolean
candidate	Candidate	boolean

json

{
  "input": {
    "sequence": "KKAAAAAA",
    "nRegionLength": 2,
    "coreWindowLength": 4,
    "minimumCoreHydropathy": 1.5
  },
  "output": {
    "coreStart": 2,
    "coreMeanHydropathy": 1.8,
    "positiveNRegion": true,
    "candidate": true
  }
}

Limitations and assumptions

No cleavage-site prediction, charge sum or cellular localization is provided. PositiveNRegion means at least one K/R, not a calculated net charge.

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. A successfully returned false flag is an evaluated outcome; its meaning is explained above.

Alternative or Complementary methods

Use Transmembrane Window Scan: Detect transmembrane helix candidates from local hydropathy windows. For a complementary task, use Mitochondrial Targeting Screen: Screen N-terminal mitochondrial targeting composition; not a localization verdict.

References

Signal Peptide Core Scan — tool.io

Similar or alternative tools

Transmembrane Window Scan
Detect transmembrane helix candidates from local hydropathy windows.
Mitochondrial Targeting Screen
Screen N-terminal mitochondrial targeting composition; not a localization verdict.