Primers & oligos

Oligo cofold (ΔG)

Minimum-free-energy structure and ΔG for one oligo (hairpin) or two oligos together (homo/heterodimer), using ViennaRNA's published loop model at a temperature you choose — DNA parameters (Mathews 2004) by default, RNA (Turner 2004) on request. Reports each strand alone, the duplex, and the interaction ΔG the two gain by pairing with each other rather than folding alone, which is the number a primer-dimer screen wants. Unlike oligo_analysis's fast stack-sum screen this is a full loop model with bulge, internal-loop and dangling-end terms; the two are on different parameter sets and must not be compared.

post/oligo_cofold

Request

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

Request body

astring required

First oligo, 5'→3'. Max 200 nt.

bstring

Second oligo. Omit to analyze hairpin structure in 'a' alone; pass the same sequence as 'a' for a homodimer.

alphabet'dna' | 'rna'

Which measured parameter set to use. This is not cosmetic — the same 20-mer can differ by several kcal/mol between them.

temperaturenumber

°C. Primer dimers matter at the annealing temperature, not at 37 °C.

partitionboolean

Also compute the ensemble free energy over all structures, not just the MFE one. Costs a second pass.

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.