Enzymes & cloning

Assembly outcomes (what else you might have built)

Enumerate the specific wrong plasmids a multi-part Golden Gate or Gibson assembly can produce — a part dropped, inverted, duplicated, two parts swapped, the backbone self-circularized — as full sequences, ranked by how few independent mis-ligations each needs. Golden Gate outcomes are annotated with the MEASURED overhang cross-talk they would have to exploit (Potapov/Pryor ligation data). Feed the result to diagnostic_digest to pick a screening enzyme. Reports no probability per outcome: the ligation data does not measure transformation or vector background.

post/assembly_outcomes

Request

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

Request body

fragmentsstring[] required

The parts in assembly order, raw or FASTA — the same list cloning_simulate takes. 2-8 parts.

namesstring[]

Optional labels for the parts, in the same order ("backbone", "promoter", "CDS"). Used in every outcome label.

method'goldengate' | 'gibson'

How the parts are joined. Golden Gate junctions are the Type IIS fusion overhangs; Gibson junctions are the homology arms.

enzymestring

Golden Gate only — the Type IIS enzyme, which fixes the overhang length (BsaI, BbsI, Esp3I (BsmBI)).

overlapLennumber

Gibson only — homology arm length, which must match what the assembly was designed with.

dataset'generic-t4-37c-1h' | 'bsai-hfv2'

Which ligation dataset to read overhang cross-talk from (Golden Gate only).

circularboolean

Circular product. Only circular assemblies are covered — a linear product's leading end is a free terminus, not a junction.

maxAlternativesnumber

Cap on returned alternatives, most accessible first. The pre-cap count is always reported as alternativesEnumerated.

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.