verify_construct

Active

declared in 1.1.0

Re-derive a construct's insert from the PCR (template + primers) claimed to have produced it, then check — independently of that claim — whether the expected insert actually appears (either orientation) in the claimed final construct, at what identity, and with exact mismatch positions if not. Optionally also checks for a premature stop in a declared reading frame. This re-derives from the claim's own stated inputs; it does not review the claim's prose.

Parameters schema

{
  "type": "object",
  "required": [
    "claimedConstruct",
    "insertTemplate",
    "insertForwardPrimer",
    "insertReversePrimer"
  ],
  "properties": {
    "insertTemplate": {
      "type": "string",
      "description": "PCR template the insert was amplified from."
    },
    "claimedConstruct": {
      "type": "string",
      "description": "The final sequence claimed to have been built."
    },
    "templateCircular": {
      "type": "boolean",
      "default": false,
      "description": "Treat insertTemplate as circular (e.g. amplifying from a plasmid)."
    },
    "expectedFrameStart": {
      "type": "integer",
      "description": "1-based position in claimedConstruct where the intended reading frame begins. If given, flags a premature stop before the end of the aligned insert region."
    },
    "insertForwardPrimer": {
      "type": "string",
      "description": "Forward primer used to amplify the insert, 5'→3'."
    },
    "insertReversePrimer": {
      "type": "string",
      "description": "Reverse primer used to amplify the insert, 5'→3'."
    },
    "maxPrimerMismatches": {
      "type": "integer",
      "default": 0,
      "description": "Mismatches tolerated per primer during PCR prediction."
    }
  },
  "additionalProperties": false
}

What this tool wraps· 0 endpoints

min confidence0.70 0.50

No endpoints wrapped at confidence ≥ 0.50.

Parent server

com.seqbench/workbench

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