---
title: "Oligo pool cross-dimer screen"
method: POST
path: "/oligo_pool_screen"
tags: ["Primers & oligos"]
---

# Oligo pool cross-dimer screen

`POST /oligo_pool_screen`

## Request

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

Screen a whole set of oligos you already have — every pair for cross-dimers, every oligo for its own hairpin and self-dimer, and the set for duplicates and Tm spread — and get back the conflicts ranked rather than a table of every combination. This is the pool-level answer cross_dimer gives one pair at a time: 51 primers is 1,275 pairs, which is 1,275 separate calls done by hand and one call done here. Not to be confused with multiplex_panel_design, which DESIGNS primers from templates; this takes the primers you have already ordered. A pairing that involves an oligo's 3' END is judged at a weaker ΔG than one that only pairs internally, because that end is where extension starts — the same two-bar rule the multiplex panel designer uses. Every number is a nearest-neighbor calculation over the sequences supplied, not a prediction of what the reaction will do.

## Request body

- object
  - `oligos` object[]: The pool, as objects with a name and a sequence. Up to 384. Use this or `fasta`, not both.
    - `name` string: Label used throughout the result. Defaults to oligo_1, oligo_2, …
    - `sequence` string, required: The oligo, 5'→3'.
  - `fasta` string: The pool as a FASTA paste (headers become the names), or as one sequence per line — which is what comes out of a spreadsheet column. An alternative to `oligos`.
  - `threePrimeThresholdDG` number: ΔG (kcal/mol) at or below which a pairing that involves a 3' END counts as a conflict.
  - `internalThresholdDG` number: The looser bar for a pairing that only sequesters primer internally, away from either 3' end.
  - `maxConflicts` integer: Conflict rows returned, most stable first. The COUNTS are always complete.
  - `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)