---
title: "Design a ribosome binding site (OSTIR)"
method: POST
path: "/rbs_design"
tags: ["Analysis"]
---

# Design a ribosome binding site (OSTIR)

`POST /rbs_design`

## Request

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

Design a 5' UTR / ribosome binding site for a given CDS. Generates a spread of Shine-Dalgarno cores and SD-to-start spacings, scores every one with OSTIR in the context of your own CDS (which matters — the rate depends on how the RBS interacts with that CDS's 5' folding), and returns them ranked. Supply targetExpression to rank by closeness to a target rate instead of by maximum strength, and supply your existing 5' UTR to get a measured baseline and fold-change for each candidate. Runs ViennaRNA on a shared service and is therefore rate limited (see 429/503).

## Request body

- object
  - `cds` string, required: Coding sequence, raw or FASTA, starting at its start codon. Only the 5' end affects the prediction, so the first ~90 nt is enough. A, C, G, T/U only. Max 10,000 nt.
  - `currentUtr` string: Optional: your existing 5' UTR (everything upstream of the start codon). Scored as a baseline so each candidate gets a fold-change against it.
  - `leader` string: Optional 5' context upstream of the designed RBS — the transcribed leader from your promoter. Affects the standby-site term. Defaults to a 20 nt unstructured poly-A leader.
  - `targetExpression` number: Optional target rate on OSTIR's arbitrary scale. Candidates are then ranked by closeness to it (log-ratio) rather than by maximum strength. Only meaningful against a number produced by this same tool.
  - `antiShineDalgarno` string: Optional anti-Shine-Dalgarno sequence (the 16S rRNA 3' end) to model a non-E. coli host. Omit to use OSTIR's own E. coli default.
  - `limit` number: How many ranked candidates to return. 1-60.

## 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)