Primers & oligos

Is the template folded over my primer site?

Fold the template around each place a primer binds, at the annealing temperature and under DNA parameters, and report how much of the primer's own footprint sits inside a helix. Primer design tools score the oligo — its Tm, its hairpin, its dimers — and leave the template unexamined, while a binding site buried in a stable stem is an ordinary reason a well-designed primer does not amplify. Returns the folded window, its free energy, the paired fraction of the footprint, and how many of the 3'-terminal five bases are paired.

post/primer_site_accessibility

Request

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

Request body

templatestring required

The template the primer has to bind — the region of interest, a plasmid, or an amplicon.

primerstring required

The primer, 5'->3'.

annealingTempnumber

The annealing temperature in Celsius. This is the whole reason the tool exists — structure at 37 C is not structure at 60 C, and the number changes the answer.

windowNtnumber

Template to fold around each site, centred on the footprint. 40-200 nt.

circularboolean

Wrap the window across the origin instead of clipping it.

maxMismatchesnumber

Mismatches allowed when locating the primer. Defaults to the binding scanner's own rate.

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.