design_lamp_primers
Design LAMP (loop-mediated isothermal amplification) primer SETS - four core oligos (F3 · B3 · FIP · BIP) plus optional loop primers, judged against Eiken's own PrimerExplorer V5 criteria. Not a pair: LAMP needs six binding regions in the published order and the distances BETWEEN them are as much of the design as the oligos. Each set comes back with the arithmetic behind its rank.
Input Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| _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. | |
| gc_max | No | GC FRACTION window, 0-1 (manual §2.3: "between about 40% to 65%") - upper bound. Unset = the preset for this template's GC class. Advanced. | |
| gc_min | No | GC FRACTION window, 0-1 (manual §2.3: "between about 40% to 65%") - lower bound. Unset = the preset for this template's GC class. Advanced. | |
| _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_sets | No | how many sets to return, best first. | |
| length_max | No | length window for the outer/inner binding regions (manual §4.2) - upper bound. Unset = the preset for this template's GC class. In nt. Advanced. | |
| length_min | No | length window for the outer/inner binding regions (manual §4.2) - lower bound. Unset = the preset for this template's GC class. In nt. Advanced. | |
| region_end | No | 0-based inclusive end. Unset = the whole sequence. Advanced. | |
| tm_loop_max | No | Tm window for the loop primers LF / LB - upper bound. Unset = the preset for this template's GC class. In °C. Advanced. | |
| tm_loop_min | No | Tm window for the loop primers LF / LB - lower bound. Unset = the preset for this template's GC class. In °C. Advanced. | |
| loop_primers | No | design LF/LB as well. They are optional in LAMP and accelerate the reaction. | |
| region_start | No | 0-based inclusive start of the region to design into (LAMP designs into a stretch, not a whole plasmid). Unset = the whole sequence; pass the selection's start to scope to it. Advanced. | |
| tm_inner_max | No | Tm window for F1c / B1c - the manual's "about 65 °C" - upper bound. Unset = the preset for this template's GC class. In °C. Advanced. | |
| tm_inner_min | No | Tm window for F1c / B1c - the manual's "about 65 °C" - lower bound. Unset = the preset for this template's GC class. In °C. Advanced. | |
| tm_outer_max | No | Tm window for F2 / B2 / F3 / B3 - the manual's "about 60 °C" - upper bound. Unset = the preset for this template's GC class. In °C. Advanced. | |
| tm_outer_min | No | Tm window for F2 / B2 / F3 / B3 - the manual's "about 60 °C" - lower bound. Unset = the preset for this template's GC class. In °C. Advanced. | |
| loop_span_max | No | 5' of F2 to 5' of F1 - the portion that forms the loop (manual §2.5: 40-60) - upper bound. Unset = the preset for this template's GC class. In bp. Advanced. | |
| loop_span_min | No | 5' of F2 to 5' of F1 - the portion that forms the loop (manual §2.5: 40-60) - lower bound. Unset = the preset for this template's GC class. In bp. Advanced. | |
| outer_gap_max | No | F3 to F2 and B3 to B2 gap. THE TWO AUTHORITIES DISAGREE here too: PrimerExplorer V5 says 0-60, the Eiken genome site 0-20 - upper bound. Unset = the preset for this template's GC class. In bp. Advanced. | |
| outer_gap_min | No | F3 to F2 and B3 to B2 gap. THE TWO AUTHORITIES DISAGREE here too: PrimerExplorer V5 says 0-60, the Eiken genome site 0-20 - lower bound. Unset = the preset for this template's GC class. In bp. Advanced. | |
| end_stability_dg | No | the terminal-6-base stability rule (manual §2.2: the ΔG "is -4 kcal/mol or less"). In kcal/mol. Advanced. | |
| end_stability_nt | No | how many terminal bases the end-stability rule measures (manual §2.2: 6). In nt. Advanced. | |
| amplified_span_max | No | F2 5' to B2 5', the amplified region. THE TWO AUTHORITIES DISAGREE: PrimerExplorer V5 says 120-160, the Eiken genome site 120-180; the default follows PrimerExplorer and this is the knob for the other reading - upper bound. Unset = the preset for this template's GC class. In bp. Advanced. | |
| amplified_span_min | No | F2 5' to B2 5', the amplified region. THE TWO AUTHORITIES DISAGREE: PrimerExplorer V5 says 120-160, the Eiken genome site 120-180; the default follows PrimerExplorer and this is the knob for the other reading - lower bound. Unset = the preset for this template's GC class. In bp. Advanced. |
Output Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| b3 | Yes | the best set's B3 outer primer | |
| f3 | Yes | the best set's F3 outer primer | |
| bip | Yes | the best set's BIP (B1c + B2), as ordered | |
| fip | Yes | the best set's FIP (F1c + F2), as ordered | |
| sets | Yes | the primer sets, best first: six regions in the literature order with every measurement that decided each one | |
| offset | Yes | where the designed-in stretch starts in the record: add it to every position above for record coordinates. 0 unless a region was given | |
| setCount | Yes | how many sets were found | |
| constraints | Yes | every window the search actually ran under, so a readout never has to restate them or guess which preset applied | |
| targetClass | Yes | which preset the search ran under - atRich, normal or gcRich, chosen from the template's own GC content (manual §4.3) | |
| penaltyTerms | Yes | what the best set's rank is MADE OF - one entry per criterion with the value measured, the window it was judged against and its cost. The costs sum to the penalty |