Cloning · experimental
Golden Gate Assembly
Digest parts with a Type IIS enzyme, match the resulting four-base overhangs, and see the construct they assemble into. Because the digestion is simulated on the real sequence, an internal site that would cut a part is found before the reaction is planned rather than after it fails.
Real 35-fragment Type-IIS build (Pryor 2020): lands already assembled at its published 65% ligation fidelity
What it does
- 01Type IIS digestion with the recognition and cut geometry of the chosen enzyme
- 02Four-base overhang matching between parts, with unmatched overhangs reported
- 03Internal-site detection, which is what makes a part undomesticated
- 04Assembled construct with carried-over annotations
- 05Multi-part assemblies in a defined order
What it runs on
Digestion and ligation run on the DnaCauldron and pydna ports in packages/ports, golden-tested against those libraries. The panel runs on @ports/goldengate, @ports/ligase, @ports/splitsite.
Everything runs client-side. Files are parsed in the browser and projects are saved on this machine, so an unpublished sequence is never uploaded.
Questions
- Which Type IIS enzymes are supported?
- Enzymes come from the bundled REBASE dataset rather than a short built-in list, so BsaI, BsmBI, Esp3I and other Type IIS enzymes are all available with their real recognition and cut geometry.
- Does it tell me when a part needs domestication?
- Yes. An internal recognition site inside a part is reported, because that site is what makes the part cut during assembly.
Also searched as
Golden Gate assembly simulator · Type IIS assembly online · BsaI assembly design · BsmBI Golden Gate · MoClo assembly simulation · overhang matching tool · modular cloning simulator · NEB Golden Gate Assembly Tool alternative · BsaI overhang design · BbsI Golden Gate assembly · overhang set fidelity check · MoClo Level 1 assembly · free Golden Gate software