Primers & oligos

In-silico PCR

Predict PCR products for a template and a pair of primers (IUPAC-aware, allows mismatches, handles circular templates). Primers may carry a non-templated 5' tail — a restriction site, a Gibson arm, a Kozak, a tag: a primer primes on its 3' end, and the tail is carried into the product rather than required to match. start/end are the TEMPLATE-derived span, length is the whole product including tails, and features marks which product bases came from the oligos (present only when there is a tail). Each end reports annealedLength and tailLength. When two primers make NO product on a template up to 60,000 bp, diagnosis says why: where each primer does prime (with the mismatched bases), which copying mistake explains one that primes nowhere (reversed but not complemented, complemented but not reversed, a base dropped or doubled, a mismatched 3' base) with the sequence that would bind, whether the two point the same way or away from each other, and the product a linear reading missed across the origin of a circle.

Batchable via POST /batch.

Chainable in workflows (passes its amplicon field to the next step).

post/in_silico_pcr

Request

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

Request body

templatestring required

Nucleotide sequence (raw or FASTA; IUPAC accepted).

forwardPrimerstring

Primer 1, 5'→3'.

reversePrimerstring

Primer 2, 5'→3' (order does not matter). Optional: one primer alone is accepted and reports the products it makes on its own — none, unless the template carries inverted sites it can prime from both ends.

maxMismatchesinteger

Mismatches tolerated per primer (0–10).

maxProductLengthinteger

Ignore predicted products longer than this (bp). A SEARCH WINDOW, not a claim about what amplifies: whole-plasmid inverse PCR — the reaction a q5-style site_directed_mutagenesis design is run as — makes one product the size of the plasmid, so raise this for a construct over 50 kb. suppressedByLength in the response counts what the window discarded.

circularboolean

Treat the template as circular (plasmid).

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

No recorded changes to this operation across all 1 revision of this API.