glycosylation_motifs read

{
  "properties": {
    "sequence": {
      "description": "Protein sequence in standard one-letter code (ACDEFGHIKLMNPQRSTVWY). Length capped at 50,000 residues. Case-insensitive; whitespace stripped.",
      "maxLength": 50000,
      "minLength": 1,
      "title": "Sequence",
      "type": "string"
    },
    "window_size": {
      "default": 12,
      "description": "Sliding-window length for O-glycosylation hotspot detection.",
      "maximum": 100,
      "minimum": 4,
      "title": "Window Size",
      "type": "integer"
    },
    "ser_thr_threshold": {
      "default": 0.5,
      "description": "Minimum Ser+Thr fraction within a window for it to count as an O-glycosylation hotspot. Default 0.5 = at least half the window is S or T.",
      "maximum": 1,
      "minimum": 0,
      "title": "Ser Thr Threshold",
      "type": "number"
    }
  },
  "required": [
    "sequence"
  ],
  "title": "GlycosylationMotifsIn",
  "type": "object"
}

{
  "$defs": {
    "NMotifHit": {
      "properties": {
        "position": {
          "description": "1-indexed position of the N residue.",
          "title": "Position",
          "type": "integer"
        },
        "motif": {
          "description": "The 3-residue N-X-[S/T] match.",
          "title": "Motif",
          "type": "string"
        }
      },
      "required": [
        "position",
        "motif"
      ],
      "title": "NMotifHit",
      "type": "object"
    },
    "OHotspot": {
      "properties": {
        "start": {
          "description": "1-indexed start of the hotspot window.",
          "title": "Start",
          "type": "integer"
        },
        "end": {
          "description": "1-indexed inclusive end of the hotspot window.",
          "title": "End",
          "type": "integer"
        },
        "ser_thr_fraction": {
          "description": "Fraction of residues in the window that are S or T.",
          "title": "Ser Thr Fraction",
          "type": "number"
        }
      },
      "required": [
        "start",
        "end",
        "ser_thr_fraction"
      ],
      "title": "OHotspot",
      "type": "object"
    }
  },
  "properties": {
    "sequence_length": {
      "description": "Length of the validated input sequence.",
      "title": "Sequence Length",
      "type": "integer"
    },
    "n_glyc_motifs": {
      "description": "N-linked glycosylation sequon hits (N-X-[S/T], X≠P).",
      "items": {
        "$ref": "#/$defs/NMotifHit"
      },
      "title": "N Glyc Motifs",
      "type": "array"
    },
    "o_glyc_hotspots": {
      "description": "O-linked glycosylation candidate windows (S/T density ≥ threshold).",
      "items": {
        "$ref": "#/$defs/OHotspot"
      },
      "title": "O Glyc Hotspots",
      "type": "array"
    },
    "n_motif_count": {
      "description": "Convenience: len(n_glyc_motifs).",
      "title": "N Motif Count",
      "type": "integer"
    },
    "o_hotspot_count": {
      "description": "Convenience: len(o_glyc_hotspots).",
      "title": "O Hotspot Count",
      "type": "integer"
    }
  },
  "required": [
    "sequence_length",
    "n_glyc_motifs",
    "o_glyc_hotspots",
    "n_motif_count",
    "o_hotspot_count"
  ],
  "title": "GlycosylationMotifsOut",
  "type": "object"
}