---
title: "What can base-pair over the ribosome binding site"
method: POST
path: "/rbs_occlusion"
tags: ["Analysis"]
---

# What can base-pair over the ribosome binding site

`POST /rbs_occlusion`

## Request

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

Find every stretch of a transcript that is reverse-complementary to the ribosome's footprint (-20 to +13 around the start codon), with the length and nearest-neighbour Tm of each duplex, and flag the ones that cover the Shine-Dalgarno core or the start codon. This is the mechanism every translational switch runs on — riboswitch, toehold switch, RNA thermometer, antisense repressor — and the first thing to look at when a switch does not switch or a construct is unexpectedly silent. Also reports where a sensor domain can be inserted without touching the site. Deterministic base-pairing, not a folding prediction: use rna_fold to ask whether a given stem actually wins at 37 °C. Reports no switching ratio — see this tool's notes for why.

## Request body

- object
  - `sequence` string, required: The transcript: the 5' UTR plus at least the start of the CDS. DNA or RNA. Max 20,000 nt.
  - `startCodonAt` integer: 1-based position of the start codon to anchor the footprint on. Omit to use the first ATG/GTG/TTG — pass it when the transcript has several, which is the usual case for a real 5' UTR.
  - `minStem` integer: Shortest duplex to report, in bp (default 6). Below 4 bp every sequence pairs with everything; a stem that actually holds a site shut is usually 8 bp or more.
  - `maxLoop` integer: Largest number of unpaired bases allowed between an arm and its target (default 100).

## 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)