---
title: "Construct auto-fix (domestication)"
method: POST
path: "/construct_autofix"
tags: ["Enzymes & cloning"]
---

# Construct auto-fix (domestication)

`POST /construct_autofix`

## Request

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

Iteratively substitutes synonymous codons to resolve unwanted restriction sites (domestication for Golden Gate), homopolymers, tandem repeats, predicted secondary structure, cryptic RBS/polyA motifs and hidden alternate-frame ORFs that construct_qc flags — without changing the encoded protein (verified). Does NOT touch premature stops or GC extremes; re-run construct_qc afterward to confirm. A native TypeScript alternative to a constraint-solver sidecar.

Batchable via `POST /batch`.

Chainable in workflows (passes its `sequence` field to the next step).

## Request body

- object
  - `sequence` string, required: Nucleotide sequence (raw or FASTA; IUPAC accepted).
  - `organism` 'ecoli' | 'human' | 'yeast' | 'cho' | 'pichia' | 'insect' | 'arabidopsis' | 'zebrafish': Codon-usage table to prefer among synonymous options.
  - `frameStart` integer: 1-based nucleotide where the reading frame begins.
  - `avoidEnzymes` string[]: Enzyme names whose internal sites should be removed (e.g. ["BsaI","BsmBI"] for Golden Gate domestication).
  - `gcWindow` integer
  - `gcLow` number
  - `gcHigh` number
  - `homopolymerMin` integer
  - `crypticOrfMinAa` integer: Minimum peptide length (aa) for a hidden alternate-frame ORF to be flagged.
  - `maxPasses` integer: Repeat full passes until clean or no further progress.

## 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)