Enzymes & cloning

Golden Gate overhang set designer

CHOOSE a set of 4-base Golden Gate/MoClo junction overhangs, rather than scoring one you already have. Maximizes the fidelity of the set's WEAKEST junction against the same published T4-ligase ligation data golden_gate_fidelity scores with, subject to every member actually ligating well — an overhang can score a perfect ratio simply because nothing was ever measured cross-reacting with it, and 94% of the ligation matrix is zeros. Pin the overhangs your vector already commits you to with fixed, forbid others with forbidden, and give junctions when the junctions sit at real positions in real sequence and may only slide a few bases. Reports whether the search was exhaustive (provably the best available) or budget-limited (the best found).

post/golden_gate_design

Request

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

Request body

countinteger required

How many junctions the assembly has, INCLUDING any given in fixed.

fixedstring[]

Overhangs that must appear — typically the ones the destination vector already commits you to. Scored like any other member; simply not swappable.

forbiddenstring[]

Overhangs the design may not use, whatever they score.

junctionsobject[]

One entry per junction still to be chosen, as {sequence, position, slide}: the construct sequence, the 1-based first base of the preferred overhang, and how many bases either side the junction may move. Use this instead of a free design when the junctions are real places in real DNA — the candidates then come from bases that actually exist. Length must equal count minus fixed.

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

Which real ligation dataset to optimize against.

minCorrectSignalnumber

Reject any overhang whose own correct-join signal is below this. Defaults to the chosen dataset's MEDIAN diagonal (2,694 for generic T4, 520 for BsaI-HFv2 — they differ five-fold, which is why this is derived rather than fixed). Set 0 to allow every overhang.

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.