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.
Input 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
| 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" |