Enzymes & cloning

Unknown plasmid: what is it and what do I plate on

Answer the question someone holding an unlabelled tube actually has, rather than returning another feature list: which antibiotic to select on, which host will carry it and at roughly what copy number, which curated backbone it resembles, and what on it will bite you later (duplicate markers, two origins for the same host, internal Type IIS sites that stop it being a Golden Gate part, long direct repeats a recA+ host can recombine out). Reads features from an annotated GenBank record when you paste one, otherwise runs the built-in signature scan. EVERY ABSENCE TRAVELS WITH THE VOCABULARY IT WAS DECIDED AGAINST: an empty marker list means nothing matched the families this screen knows, never that the plasmid cannot be selected — run plasmid_deep_annotate, whose library is far larger, before concluding that.

post/plasmid_dossier

Request

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

Request body

sequencestring required

Nucleotide sequence (raw or FASTA; IUPAC accepted).

circularboolean

Treat the query as a circular molecule (most plasmids are).

minRepeatLengthinteger

Shortest direct repeat (bp) to raise as a recombination hazard. Below ~20 bp chance matches multiply and recombination has little to work with.

goldenGateEnzymesstring[]

Type IIS enzymes you intend to assemble with (e.g. ["BsaI"]). Internal sites are ALWAYS reported in typeIISSites — random sequence carries them and so does nearly every real plasmid — but they only become a hazard for an enzyme named here, so the hazard list stays worth reading.

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.