Oligo cofold (ΔG)
oligo_cofoldMinimum-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. PREDICTED, NOT MEASURED. No skill statistic is claimed for predicting whether a PCR fails. Loop-model MFE folding reproduces measured structure well for short duplexes and progressively worse with length; the ΔG itself carries roughly kcal/mol-scale uncertainty and the MFE structure is one structure out of an ensemble — request partition for the ensemble free energy, which is the more honest single number when several structures compete. Valid for: short oligos, at most 200 nt per strand, at the temperature given. It models two strands in isolation at no particular concentration: it does not know your primer concentration, salt, or cycling programme, so it cannot say whether a dimer will actually form in your tube.
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| a | Yes | First oligo, 5'→3'. Max 200 nt. | |
| b | No | Second oligo. Omit to analyse hairpin structure in 'a' alone; pass the same sequence as 'a' for a homodimer. | |
| alphabet | No | Which measured parameter set to use. This is not cosmetic — the same 20-mer can differ by several kcal/mol between them. | dna |
| partition | No | Also compute the ensemble free energy over all structures, not just the MFE one. Costs a second pass. | |
| temperature | No | °C. Primer dimers matter at the annealing temperature, not at 37 °C. |