golden_gate_fidelity

Active

declared in 1.1.0

Score a candidate set of 4-base Golden Gate/MoClo junction overhangs against real published T4-ligase ligation-count data: per-overhang specificity, the weakest link in the set, and any risky cross-reacting pairs. Optionally compare against a named published overhang set. This is SeqBench's own transparent scoring methodology — it does not reproduce NEB's/Potapov's own published aggregate fidelity percentages for named sets (their exact formula isn't disclosed anywhere accessible).

Parameters schema

{
  "type": "object",
  "required": [
    "overhangs"
  ],
  "properties": {
    "dataset": {
      "enum": [
        "generic-t4-37c-1h",
        "bsai-hfv2"
      ],
      "type": "string",
      "default": "generic-t4-37c-1h",
      "description": "Which real ligation dataset to score against — generic T4 ligase, or an enzyme-specific one-pot dataset if that matches your actual digestion enzyme."
    },
    "overhangs": {
      "type": "array",
      "items": {
        "type": "string"
      },
      "description": "The candidate 4-base overhangs for one assembly (e.g. [\"GGAG\",\"TACT\",\"AATG\"]). At least 2, no duplicates."
    },
    "riskThreshold": {
      "type": "number",
      "default": 0.05,
      "description": "Flag a pair as risky when the cross-reaction is at least this fraction of that pair's own total signal."
    },
    "compareToNamedSet": {
      "enum": [
        "pryor-2020-plant-11",
        "pryor-2020-20set",
        "cidar-moclo"
      ],
      "type": "string",
      "description": "Also score this published reference set (see namedSetsAvailable in the output) alongside your candidate set, for comparison."
    }
  },
  "additionalProperties": false
}

What this tool wraps· 0 endpoints

min confidence0.70 0.50

No endpoints wrapped at confidence ≥ 0.70.

Parent server

com.seqbench/workbench

1/7 registries

View full server →