---
title: "In-silico PCR"
method: POST
path: "/in_silico_pcr"
tags: ["Primers & oligos"]
---

# In-silico PCR

`POST /in_silico_pcr`

## Request

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

Predict PCR products for a template and a pair of primers (IUPAC-aware, allows mismatches, handles circular templates). Primers may carry a non-templated 5' tail — a restriction site, a Gibson arm, a Kozak, a tag: a primer primes on its 3' end, and the tail is carried into the product rather than required to match. start/end are the TEMPLATE-derived span, `length` is the whole product including tails, and `features` marks which product bases came from the oligos (present only when there is a tail). Each end reports annealedLength and tailLength. When two primers make NO product on a template up to 60,000 bp, `diagnosis` says why: where each primer does prime (with the mismatched bases), which copying mistake explains one that primes nowhere (reversed but not complemented, complemented but not reversed, a base dropped or doubled, a mismatched 3' base) with the sequence that would bind, whether the two point the same way or away from each other, and the product a linear reading missed across the origin of a circle.

Batchable via `POST /batch`.

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

## Request body

- object
  - `template` string, required: Nucleotide sequence (raw or FASTA; IUPAC accepted).
  - `forwardPrimer` string: Primer 1, 5'→3'.
  - `reversePrimer` string: Primer 2, 5'→3' (order does not matter). Optional: one primer alone is accepted and reports the products it makes on its own — none, unless the template carries inverted sites it can prime from both ends.
  - `maxMismatches` integer: Mismatches tolerated per primer (0–10).
  - `maxProductLength` integer: Ignore predicted products longer than this (bp). A SEARCH WINDOW, not a claim about what amplifies: whole-plasmid inverse PCR — the reaction a q5-style site_directed_mutagenesis design is run as — makes one product the size of the plasmid, so raise this for a construct over 50 kb. `suppressedByLength` in the response counts what the window discarded.
  - `circular` boolean: Treat the template as circular (plasmid).

## 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)