Oligo pool cross-dimer screen
oligo_pool_screenScreen a whole set of oligos you already have — every pair for cross-dimers, every oligo for its own hairpin and self-dimer, and the set for duplicates and Tm spread — and get back the conflicts ranked rather than a table of every combination. This is the pool-level answer cross_dimer gives one pair at a time: 51 primers is 1,275 pairs, which is 1,275 separate calls done by hand and one call done here. Not to be confused with multiplex_panel_design, which DESIGNS primers from templates; this takes the primers you have already ordered. A pairing that involves an oligo's 3' END is judged at a weaker ΔG than one that only pairs internally, because that end is where extension starts — the same two-bar rule the multiplex panel designer uses. Every number is a nearest-neighbour calculation over the sequences supplied, not a prediction of what the reaction will do.
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| mgMM | No | Divalent cation [Mg2+] (mM). | |
| naMM | No | Monovalent cation [Na+]/[K+] (mM). | |
| fasta | No | The pool as a FASTA paste (headers become the names), or as one sequence per line — which is what comes out of a spreadsheet column. An alternative to `oligos`. | |
| dntpMM | No | Total [dNTP] (mM), chelates Mg2+. | |
| oligos | No | The pool, as objects with a name and a sequence. Up to 384. Use this or `fasta`, not both. | |
| oligoNM | No | Total strand concentration (nM). | |
| maxConflicts | No | Conflict rows returned, most stable first. The COUNTS are always complete. | |
| internalThresholdDG | No | The looser bar for a pairing that only sequesters primer internally, away from either 3' end. | |
| threePrimeThresholdDG | No | ΔG (kcal/mol) at or below which a pairing that involves a 3' END counts as a conflict. |