---
title: "Primer designer"
method: POST
path: "/primer_design"
tags: ["Primers & oligos"]
---

# Primer designer

`POST /primer_design`

## Request

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

De-novo PCR primer design (Primer3-style penalty picker): enumerate and score candidate primer pairs against length/Tm/GC/3'-clamp/structure constraints.

## Request body

- object
  - `template` string, required: Nucleotide sequence (raw or FASTA; IUPAC accepted).
  - `lenMin` integer
  - `lenOpt` integer
  - `lenMax` integer
  - `tmMin` number
  - `tmOpt` number
  - `tmMax` number
  - `tmMaxDiff` number: Max Tm difference within a pair (°C).
  - `gcMin` number
  - `gcMax` number
  - `ampliconMin` integer
  - `ampliconMax` integer
  - `targetStart` integer: 1-based inclusive start of a region the product must span (optional).
  - `targetEnd` integer: 1-based inclusive end of the target region (optional).
  - `maxReturn` integer: Number of best pairs to return.
  - `maxPolyX` integer: Longest run of one base a primer may contain (Primer3's PRIMER_MAX_POLY_X). Omitted or 0 means no limit.
  - `gcClamp` integer: Consecutive G/C required at the very 3' end (Primer3's PRIMER_GC_CLAMP). Omitted or 0 means no requirement.
  - `minThreePrimeDG` number: Floor on the NN ΔG37 (kcal/mol) of the five 3'-most bases; a more stable end than this is rejected. Deliberately not Primer3's max_end_stability, which is a different scale this model has not been calibrated against.
  - `excludedRegions` object[]: Regions no primer may overlap, 1-based inclusive, as {start,end}. start > end is a region crossing the origin of a circular template.
    - `start` integer, required
    - `end` integer, required
  - `oligoNM` number: Total strand concentration (nM).
  - `naMM` number: Monovalent cation [Na+]/[K+] (mM).
  - `mgMM` number: Divalent cation [Mg2+] (mM).
  - `dntpMM` number: Total [dNTP] (mM), chelates Mg2+.

## 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)