O Glycosylation Windows

Find Ser/Thr-rich windows as O-glycosylation context candidates.

Description

Ser/Thr-rich sequence windows provide a simple O-glycosylation-context screen.

Ser/Thr-rich sequence windows provide a simple O-glycosylation-context screen. Their composition is a candidate feature rather than evidence of attached glycans.^[1]

Find Ser/Thr-rich windows as O-glycosylation context candidates.

When to use O Glycosylation Windows

Use this tool to find Ser/Thr-rich windows as O-glycosylation context candidates.

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 O Glycosylation 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, minimumSerThrFraction using the field table and calculation rules, then run the tool.
Read candidateStarts, maximumSerThrFraction. 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
minimumSerThrFraction	Minimum ser thr fraction	number	Required

Enter a canonical sequence, safe-integer window within its length and minimum fraction in 0–1. Slide by one residue; return zero-based qualifying starts and maximum fraction.

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.

fraction_i=(S+T count in window_i)/windowLength; qualifies if fraction_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
maximumSerThrFraction	Maximum ser thr fraction	number

json

{
  "input": {
    "sequence": "SSSTAA",
    "windowLength": 3,
    "minimumSerThrFraction": 0.6666666666666666
  },
  "output": {
    "candidateStarts": [
      0,
      1,
      2
    ],
    "maximumSerThrFraction": 1
  }
}

Limitations and assumptions

Overlapping windows are retained. Modification occupancy, enzyme specificity and glycan structure are not determined.

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 N Glycosylation Sequons: Locate N-X-S/T glycosylation sequons excluding proline in the X site. For a complementary task, use Phosphorylation Sites: Count potential Ser/Thr/Tyr phosphorylation positions.

References

O Glycosylation Windows — tool.io

Similar or alternative tools

N Glycosylation Sequons
Locate N-X-S/T glycosylation sequons excluding proline in the X site.
Phosphorylation Sites
Count potential Ser/Thr/Tyr phosphorylation positions.