check_primer_specificity
Read-only
Check primer pairs for products off their template, the way NCBI Primer-BLAST does, and rank them by it: each distinct primer is searched against a sequence database at EMBL-EBI with short-query BLAST, hits are paired into products by Primer-BLAST's own mismatch rule, and the template is searched too so the record identical to it is recognized as the intended target. Pairs with no product elsewhere rank first, in the order given, then pairs not checked, then pairs with a named unintended product. Primer sequences and the template LEAVE THE MACHINE; the database is a collection, not an assembled genome, and cannot be filtered by organism.
Input Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| No | EBI requires a contact address on every submission (their abuse contact, not a login). Left empty, the one saved in any EMBL-EBI panel is used. | ||
| pairs | No | several pairs to rank, one per line as `forward reverse` (whitespace or a comma between), in their design order. Taken instead of forward/reverse when given. | |
| top_n | No | how many of the pairs, from the top, to search. The rest rank as unchecked. At most 14, so the batch stays inside EMBL-EBI's 30 searches. | |
| _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. | |
| forward | No | one pair's forward primer, 5'→3' (wire design_primers' `forward`). | |
| reverse | No | that pair's reverse primer, 5'→3' (wire design_primers' `reverse`). | |
| _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. | |
| database | No | the nucleotide database id, as the service names it (em_all, em_rel_hum…). Left empty, the service's OWN nucleotide default is used and reported back. | |
| template | No | the sequence the pairs were designed on. Searched too: the database record identical to it is where the intended product lives. Left empty, the open record is used; with neither, every product counts as unintended and the result says so. |
Output Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| ranked | Yes | every pair in ranked order: its design rank, standing (specific, unchecked, non-specific), intended products and unintended products with subject, span, length and mismatches | |
| forward | Yes | the top-ranked pair's forward primer (wire into pcr_amplify) | |
| reverse | Yes | the top-ranked pair's reverse primer | |
| identical | Yes | database records identical to the template, whose products are the intended ones | |
| specificCount | Yes | pairs with no product off the template; wire into a $when to branch on "any specific pair" |