cloning_simulate

Parameters schema

{
  "type": "object",
  "required": [
    "method"
  ],
  "properties": {
    "names": {
      "type": "array",
      "items": {
        "type": "string"
      },
      "description": "Optional labels for each fragment."
    },
    "enzyme": {
      "type": "string",
      "default": "BsaI",
      "description": "Type IIS enzyme for Golden Gate (e.g. BsaI, BbsI, Esp3I (BsmBI))."
    },
    "insert": {
      "type": "string",
      "description": "Insert sequence (restriction method)."
    },
    "method": {
      "enum": [
        "gibson",
        "goldengate",
        "restriction",
        "topo"
      ],
      "type": "string",
      "default": "gibson",
      "description": "Assembly method."
    },
    "vector": {
      "type": "string",
      "description": "Vector sequence (restriction method)."
    },
    "enzyme3": {
      "type": "string",
      "default": "BamHI",
      "description": "Insert 3′ enzyme (restriction method)."
    },
    "enzyme5": {
      "type": "string",
      "default": "EcoRI",
      "description": "Insert 5′ enzyme (restriction method)."
    },
    "circular": {
      "type": "boolean",
      "default": true,
      "description": "Produce a circular product."
    },
    "topoMode": {
      "enum": [
        "ta",
        "blunt",
        "directional"
      ],
      "type": "string",
      "default": "ta",
      "description": "TOPO chemistry (topo method): TA (Taq 3′-A), blunt, or directional (pENTR/D-TOPO, needs 5′-CACC on the insert)."
    },
    "fragments": {
      "type": "array",
      "items": {
        "type": "string"
      },
      "description": "Fragments (5′→3′), assembled head-to-tail. Used by gibson/goldengate."
    },
    "overlapLen": {
      "type": "integer",
      "default": 20,
      "description": "Gibson homology-arm length (bp)."
    },
    "armTmTarget": {
      "type": "number",
      "default": 60,
      "description": "Target annealing Tm (°C) for primer arms."
    },
    "vectorEnzyme3": {
      "type": "string",
      "description": "Vector 3′ enzyme (restriction method); defaults to enzyme3."
    },
    "vectorEnzyme5": {
      "type": "string",
      "description": "Vector 5′ enzyme (restriction method); defaults to enzyme5. Set a different, compatible enzyme (e.g. BglII for a BamHI insert) to model heterologous-overhang cloning."
    },
    "dephosphorylateVector": {
      "type": "boolean",
      "default": false,
      "description": "CIP/rSAP-dephosphorylate the vector to suppress self-ligation background (restriction method)."
    }
  },
  "additionalProperties": false
}

No endpoints wrapped at confidence ≥ 0.50.

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