---
title: "CRISPR guide off-target check"
method: POST
path: "/crispr_offtarget_check"
tags: ["CRISPR"]
---

# CRISPR guide off-target check

`POST /crispr_offtarget_check`

## Request

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

Screen a guide's protospacer for off-target sites (protospacer match + valid PAM, both strands) against a small curated set of common lab reference genomes (see genomesChecked) — NOT a whole human/mouse genome search. For SpCas9 with a 20 nt spacer each site also gets a Doench 2016 CFD score, so sites are ranked by predicted cut likelihood rather than by mismatch count alone, and the guide gets an aggregate specificity. Use this the same way primer_specificity is used: a useful sanity check within the covered organisms, not a clearance guarantee for a mammalian expression host.

## Request body

- object
  - `protospacer` string, required: The guide's protospacer sequence, 5'→3' (no PAM). Max 32 nt — every supported nuclease uses a 20–23 nt guide.
  - `nuclease` 'spcas9' | 'spcas9ng' | 'sacas9' | 'cas12a': Nuclease id — determines the PAM pattern/side required at each candidate site.
  - `maxMismatches` integer: Mismatches tolerated between the protospacer and a candidate genomic site. Max 4 — a complete search seeds on maxMismatches+1 non-overlapping blocks, and past that the blocks are too short to be selective against a multi-Mb genome (a site that mismatched more would not be cut anyway).

## 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)