GPI Anchor Signal Screen

Screen C-terminal omega site and hydrophobic tail for a GPI-anchor signal.

Description

A GPI-anchor signal screen fixes a candidate omega site immediately before a selected C-terminal tail.

A GPI-anchor signal screen fixes a candidate omega site immediately before a selected C-terminal tail. Tail composition and omega identity are tested together.^[1]

Screen C-terminal omega site and hydrophobic tail for a GPI-anchor signal.

When to use GPI Anchor Signal Screen

Use this tool to screen C-terminal omega site and hydrophobic tail for a GPI-anchor signal.

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 GPI Anchor Signal Screen 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, tailLength, hydrophobicResidues, minimumTailHydrophobicFraction using the field table and calculation rules, then run the tool.
Read omegaIndex, tailHydrophobicFraction, 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
tailLength	Tail length	number	Required
hydrophobicResidues	Hydrophobic residues	string	Required
minimumTailHydrophobicFraction	Minimum tail hydrophobic fraction	number	Required

Enter a canonical sequence, positive safe-integer tail length shorter than it, case-sensitive hydrophobic residue set and minimum fraction in 0–1. Return zero-based omega index, tail fraction and combined flag.

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.

omegaIndex=length−tailLength−1; candidate=omega in SACGN AND tailFraction≥minimum

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

Output field	Meaning	Value type
omegaIndex	Omega index	number
tailHydrophobicFraction	Tail hydrophobic fraction	number
candidate	Candidate	boolean

json

{
  "input": {
    "sequence": "ASAAAAAA",
    "tailLength": 6,
    "hydrophobicResidues": "AILMVF",
    "minimumTailHydrophobicFraction": 0.75
  },
  "output": {
    "omegaIndex": 1,
    "tailHydrophobicFraction": 1,
    "candidate": true
  }
}

Limitations and assumptions

No spacer model, site search, processing reaction or measured anchoring is included. The selected tail fixes the tested site.

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 KDEL Retention Signal: Detect a C-terminal KDEL ER retention signal. For a complementary task, use Transmembrane Window Scan: Detect transmembrane helix candidates from local hydropathy windows.

References

GPI Anchor Signal Screen — tool.io

Similar or alternative tools

KDEL Retention Signal
Detect a C-terminal KDEL ER retention signal.
Transmembrane Window Scan
Detect transmembrane helix candidates from local hydropathy windows.