---
title: "Golden Gate overhang fidelity"
method: POST
path: "/golden_gate_fidelity"
tags: ["Enzymes & cloning"]
---

# Golden Gate overhang fidelity

`POST /golden_gate_fidelity`

## Request

- Base URL: `https://seqbench.com/api/v1`
- URL: `https://seqbench.com/api/v1/golden_gate_fidelity`
- Auth: none required

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).

## Request body

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

## Response `200`

Tool ran successfully.

- SuccessResponse: Standard success envelope returned by every single-tool call.
  - `ok` unknown, required
  - `tool` string, required: The tool slug that ran.
  - `result` object, required: Tool-specific output object. Its shape depends on the tool — call `GET /{tool}` or see the docs for each tool's fields.
  - `gate` GateResult
    - `pass` boolean, required: True if and only if every hard check passed.
    - `checks` GateCheck[], required
      - `id` string, required
      - `label` string, required
      - `severity` 'hard' | 'soft', required
      - `pass` boolean, required
      - `message` string, required
      - `value` number
      - `threshold` string
    - `notChecked` string[], required: Honest list of what this gate does NOT verify.
  - `provenance` Provenance, required
    - `apiVersion` string, required
    - `tool` union, required: Tool slug, or an array of slugs (one per step) for a workflow.
      - string
      - string[]
    - `generatedAt` string, date-time, required: ISO 8601 timestamp of when the result was generated.

## Other responses

- `400`: Invalid argument or the tool could not run.
- `404`: Unknown tool.
- `429`: Rate limited (metered tools only). Body carries code `rate_limited` and retryable `true`; honor the Retry-After header.
- `503`: A metered tool is momentarily at capacity. The identical request should succeed after Retry-After; body carries code `upstream_unavailable`.

---

[API](https://skmtc.dev/seqbench/apis/seqbench-api.md) · [All operations](https://skmtc.dev/seqbench/apis/seqbench-api/llms.txt) · [OpenAPI document](https://skmtc.dev/seqbench/apis/seqbench-api/revisions/132575216865?raw)