Primers & oligos

Check an oligo order against its map

Check a list of oligos against the plasmid or template they were designed from, before ordering them. For each oligo: where it primes (3'-anchored, so cloning tails are allowed), on which strand, and which bases disagree with the map. When an oligo primes nowhere it says WHICH copying mistake explains it — reversed without being complemented, complemented without being reversed, one base dropped or doubled, a wrong last base — and gives the sequence that was meant, but only when exactly one such mistake reproduces an oligo that binds. It simulates every product the order can make (up to 15,000 bp) with the in_silico_pcr engine, and for pairs the names declare (GFP_F / GFP_R) says why they make none, including which of the two is written as the wrong strand. Also flags one sequence under two names, one name on two sequences, a primer saved in the map under the same name that sits elsewhere, and 3' self-dimers/hairpins. Up to 96 oligos.

post/oligo_order_check

Request

  • Base URL: https://seqbench.com/api/v1
  • URL: https://seqbench.com/api/v1/oligo_order_check
  • Auth: none required

Request body

templatestring required

The map the oligos were designed from — a GenBank record (its LOCUS line gives the topology and its features name where each oligo sits), FASTA, or bare sequence.

oligosstring required

The order sheet: FASTA (headers become names), or one oligo per line as name<TAB or comma or space>sequence, or bare sequences one per line (named oligo_1, oligo_2, …).

circularboolean

Override the topology. Omitted: a GenBank/EMBL record's own header decides, and bare sequence is treated as a circular plasmid (stated in the response as topologySource).

Response

Tool ran successfully.

okunknown required
toolstring required

The tool slug that ran.

resultobject required

Tool-specific output object. Its shape depends on the tool — call GET /{tool} or see the docs for each tool's fields.

Example response

{
  "provenance": {
    "apiVersion": "1.1.0"
  }
}

Changes