Primers & oligos

Multiplex PCR panel design

Choose one primer pair per target so the whole panel works in one tube: no cross-dimer between any two of the primers, every amplicon resolvable from every other on the gel you will run, and one annealing temperature that serves all of them. Searches combinations rather than picking each target's best pair in isolation, which is what makes panels fail — and when no compatible panel exists it names the target pairs that cannot be multiplexed at all, so you know which one to redesign.

post/multiplex_panel_design

Request

  • Base URL: https://seqbench.com/api/v1
  • URL: https://seqbench.com/api/v1/multiplex_panel_design
  • Auth: none required

Request body

agarosePercentnumber

Gel the panel will be read on. Omit and the percentage whose resolving window contains the amplicons is chosen and reported — a panel of small products judged on a 1% gel reads as all-comigrating, which is about the gel rather than the primers.

dimerThresholdDGnumber

ΔG (kcal/mol) at or below which a cross-dimer involving a primer's 3' END is a conflict. That end is where extension starts, so it matters at a weaker ΔG than an internal pairing.

internalDimerThresholdDGnumber

The looser bar for a cross-dimer that pairs internally and only sequesters primer.

maxTmSpreadnumber

Widest Tm difference tolerated across every primer in the panel, in °C — one annealing temperature has to serve all of them.

candidatesPerTargetnumber

Candidate pairs considered per target (max 6). More finds a panel where fewer cannot, at the cost of a larger search.

ampliconMinnumber

Panel-wide default product size floor, for targets that set none.

ampliconMaxnumber

Panel-wide default product size ceiling.

Response

Tool ran successfully.

okunknown required
toolstring required

The tool slug that ran.

resultobject required

Tool-specific output object. Its shape depends on the tool — call GET /{tool} or see the docs for each tool's fields.

Example response

{
  "provenance": {
    "apiVersion": "1.1.0"
  }
}

Changes

No recorded changes to this operation across all 1 revision of this API.