screen_oligo_structure
Read-only
Fold a set of oligos and check them against each other: every oligo's hairpin, its self-dimer anywhere and its self-dimer at the 3' end, plus the cross-dimer with every other oligo in the set, at any position and at a 3' end. This is primer3's thal — the same engine the Tm columns elsewhere use — so a pool can be screened before it is ordered rather than explained after a gel. The 3'-end measures are the ones that matter for a primer-dimer BAND, because only a paired 3' end extends. Works on any oligo: primers, probes, ssODN donors, guides, adapters.
Input Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| names | No | optional labels, in the same order as `oligos` — what the pair table calls each one. Missing or short, the rest are numbered. Advanced. | |
| _files | No | The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name. | |
| oligos | Yes | the oligos to screen, 5'→3'. One is a valid pool: it still gets its hairpin and self-dimer. Wire the primers out of a design run, or list them. | |
| dv_conc | No | divalent cations (Mg²⁺), mM. In mM. | |
| mv_conc | No | monovalent cations (Na⁺ + K⁺ + Tris⁺), mM. In mM. | |
| _subject | No | The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several. | |
| dna_conc | No | oligo strand concentration, nM — it moves a DIMER's Tm and leaves a hairpin's alone, because a hairpin is unimolecular. In nM. | |
| max_loop | No | largest internal loop the alignment will span (primer3's MAX_LOOP). Advanced. | |
| dntp_conc | No | total dNTPs, mM — subtracted from the divalent term, because dNTPs chelate Mg²⁺. In mM. | |
| temperature | No | the temperature ΔG is evaluated at. It does NOT move any Tm — Tm is the structure's own melting point — so change it to read ΔG at your annealing temperature. In °C. Advanced. |
Output Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| clean | Yes | the oligos that broke no limit of their own AND appear in no flagged pair — the ones to order. An oligo is dropped from here for a partner's sake, which is the point of screening a POOL | |
| pairs | Yes | every unordered pair INCLUDING the self diagonal, with the any-position and 3'-end cross-dimer and which oligo's 3' end the reported end measure belongs to | |
| limits | Yes | the five primer3 cutoffs every verdict here was made against, and the settings file they come from — a verdict whose threshold is not stated is not checkable (§10a) | |
| flagged | Yes | only the oligos and pairs that broke a limit, with which limit — the list to act on. Empty is a real result and means every measure sat under primer3's cutoffs | |
| perOligo | Yes | per oligo: its hairpin, its self-dimer anywhere and its 3'-end self-dimer, each with ΔG, ΔH, ΔS, Tm, the limit it was graded against and whether it exceeds it — plus primer3's own drawing of the pairing, so a number can be checked rather than trusted | |
| conditions | Yes | the buffer every number here was computed in, including the values left at their default — so a result carries its own reaction rather than an unstated one | |
| provenance | Yes | which primer3 this engine IS, and which one a user comparing against primer3web or bioconda `ntthal` is holding. The two generations disagree on about 3% of primer-length oligos | |
| worstAnyTmC | Yes | the highest any-position dimer melting temperature in the set, self-dimers included | |
| worstEndTmC | Yes | the highest 3'-end dimer melting temperature in the set — the single number that predicts a primer-dimer band. Self-dimers count, because an oligo dimerising with itself makes a band too. 0 means no 3'-anchored alignment was found at all, not that the set is safe | |
| worstHairpinTmC | Yes | the highest hairpin melting temperature across the oligos — a hairpin melting above the annealing temperature competes with the template | |
| incompatibleCount | Yes | how many DISTINCT pairs broke a limit — the self diagonal excluded, because a single oligo's self-dimer is not a pair problem and counting it makes a one-oligo run report an incompatibility. Branch a workflow on this rather than re-deriving it from `pairs`; read `flagged` for the self-structures |