multiplex_pcr
Read-only
Screen a primer POOL against one or more templates: every predicted product, per-primer off-target binding, the pairs that tell templates apart on a gel, and the all-against-all primer-dimer matrix a pool actually lives or dies by (pydna primer_screen + primer3 thal).
Input Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| pool | No | also partition the screened reactions into compatible tubes (MultiPLX grouping), judged by the preset and cutoffs below. | |
| limit | No | minimum 3' footprint match for a primer to be considered bound (pydna's own default is 16). In bp. | |
| _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. | |
| primers | No | the primer pool — literal sequences, or wire primer outputs from upstream design nodes. | |
| _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. | |
| max_size | No | largest product to report. In bp. | |
| min_size | No | smallest product to report. In bp. | |
| templates | No | extra templates to screen against — wire records or name library documents (the subject is included by default). | |
| conditions | No | the reaction buffer every temperature here is computed in - Na+/K+/Tris/Mg2+/dNTPs, the primer concentration, the salt-correction method and the melting model. Left unset it is filled from your reaction-conditions settings, so this node and the PCR panel describe ONE tube; with neither it falls back to pydna's Taq defaults, which is what every golden was captured under. Advanced. | |
| max_groups | No | most tubes the pool may be split into. Only applies when pool is true. | |
| cutoffs_off | No | cutoffs to switch off (not applied at all), whatever the preset says. Only applies when pool is true. Advanced. | |
| pool_preset | No | which authority's limits a tube is judged by: MultiPLX's three stringencies, or primer3's own structural limits (calibrated for the ΔG engine computing the scores). Only applies when pool is true. | normal |
| max_per_group | No | most reactions one tube may hold. Only applies when pool is true. | |
| include_subject | No | screen against the node's subject as a template. | |
| cutoff_max_tm_diff | No | Primer Tm spread [°C]: Largest primer Tm difference allowed inside a tube: one annealing temperature has to work for every reaction in it. Unset keeps the preset's value. In °C. Only applies when pool is true. Advanced. | |
| cutoff_prim_prim_any | No | Primer–primer, anywhere [kcal/mol]: Any duplex between two primers. Not extendable on its own, but it takes primer out of the reaction. Unset keeps the preset's value. In kcal/mol. Only applies when pool is true. Advanced. | |
| cutoff_prim_prod_any | No | Primer–product, anywhere [kcal/mol]: Any duplex between a primer and another reaction’s amplicon. Unset keeps the preset's value. In kcal/mol. Only applies when pool is true. Advanced. | |
| cutoff_prim_prim_end1 | No | Primer–primer, one 3′ end [kcal/mol]: One primer's 3′ end anneals anywhere on the other. Extendable, so it competes with the template. Unset keeps the preset's value. In kcal/mol. Only applies when pool is true. Advanced. | |
| cutoff_prim_prim_end2 | No | Primer–primer, both 3′ ends [kcal/mol]: A blunt 3′–3′ dimer: each primer can extend on the other, so the pair consumes itself and makes a short artefact band. Unset keeps the preset's value. In kcal/mol. Only applies when pool is true. Advanced. | |
| cutoff_prim_prod_end1 | No | Primer–product, 3′ end [kcal/mol]: A primer's 3′ end annealing inside another reaction's amplicon: it primes on the wrong molecule. Unset keeps the preset's value. In kcal/mol. Only applies when pool is true. Advanced. | |
| cutoff_max_prod_len_diff | No | Band spread (range) [bp]: Products in one tube must differ by no more than this, so one extension time suits them all. Unset keeps the preset's value. In bp. Only applies when pool is true. Advanced. | |
| cutoff_min_prod_len_diff | No | Band separation (ladder) [bp]: Products in one tube must differ by at least this much, or the bands co-migrate and you cannot tell which reaction worked. Unset keeps the preset's value. In bp. Only applies when pool is true. Advanced. | |
| cutoff_max_prim_prim_any_tm | No | Cross-dimer Tm, anywhere [°C]: primer3's own limit, on the scale our ΔG engine is calibrated for. A dimer melting above this competes with template annealing. Unset keeps the preset's value. In °C. Only applies when pool is true. Advanced. | |
| cutoff_max_prim_prim_end_tm | No | Cross-dimer Tm, 3′ end [°C]: primer3's limit for the 3′-end dimer: the configuration that extends. Unset keeps the preset's value. In °C. Only applies when pool is true. Advanced. |
Output Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| pools | Yes | with `pool` on: the tubes, the per-tube verification, and a refusal naming the limit and pair that forced it when no partition fits | |
| dimerMap | Yes | the all-against-all dimer ΔG as a heatmap, the most stable structure each pair forms anywhere along the oligos | |
| amplicons | Yes | every predicted product (which pair, which template, what size) | |
| poolCount | Yes | with `pool` on: how many tubes the partition needed (0 when it refused) | |
| crossDimers | Yes | all-against-all primer-dimer matrix, or null with fewer than two primers | |
| diagnostics | Yes | pairs that discriminate the templates by product size | |
| primerStats | Yes | per-primer binding counts, including off-target | |
| ampliconCount | Yes | number of predicted products |