---
title: "Codon optimizer"
method: POST
path: "/codon_optimize"
tags: ["Codon usage"]
---

# Codon optimizer

`POST /codon_optimize`

## Request

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

Codon-optimize a protein (or coding DNA) for an expression host by picking the most-frequent codon per residue.

Batchable via `POST /batch`.

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

## Request body

- object
  - `protein` string, required: Protein sequence (one-letter codes). Coding DNA/RNA is accepted and translated in frame +1 up to the first stop codon (residues after an in-frame stop are NOT optimized).
  - `organism` 'ecoli' | 'human' | 'yeast' | 'cho' | 'pichia' | 'insect' | 'arabidopsis' | 'zebrafish'
  - `inputType` 'auto' | 'protein' | 'dna': How to read `protein`. 'auto' guesses from the alphabet (>90% ACGTUN reads as DNA), which mis-files genuine Ala/Cys/Gly/Thr/Asn-only peptides — set 'protein' or 'dna' to force it.

## 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)