Grammar assembly plan

A multi-part Type IIS build drawn as the graph it is — which parts join at which fusion site, in the order the overhangs force.

What it doesCopy Anchor Link

A Golden Gate or MoClo reaction is not a list of parts, it is an ordered set of joins, and the order is not something you choose. Each part carries 4 bp overhangs left by the Type IIS enzyme, and two parts can only be adjacent if one's right overhang matches the other's left. The assembly is therefore determined by the overhangs, and the useful question — what will actually come out of this tube, and in what arrangement — is a question about a graph.

This is that graph for the product you have selected. Each level is one step, an edge is a part going into the join below it, and the edge is labelled with the fusion site that makes the join. Reading left to right gives the order the fragments end up in; reading down gives the levels of a hierarchical build.

The value of seeing it rather than reading a part list is that a wrong assembly usually looks right in a list. Two parts with an accidentally shared overhang produce a plausible-looking set of names and a construct in the wrong order, and the order is visible here.

When you'd use thisCopy Anchor Link

• Before ordering synthesis. The arrangement the overhangs force is what you will get, and it is cheaper to notice a transposed pair now.
• When a build produces an unexpected product. The graph shows which junction did something you did not intend.
• When designing a multi-level build. A hierarchical assembly's levels are the shape of the work — which sub-assemblies must exist before the final reaction.
• To check an acceptor is where you think. A backbone that joined at the wrong end is an arrangement error, not a sequence error, and does not show up in a length.

What this computesCopy Anchor Link

• The assembly graph of the selected product: its levels, the parts on each, and the edges between them, from the simulated reaction rather than from the order the parts were listed in.
• The fusion site on every edge — the 4 bp overhang that joins those two parts, which is the reason the order is forced.
• The product's own facts: its length, whether it closed circular, and how many parts it consumed.
• The enzyme in force, because the overhangs and therefore the whole arrangement are its.

What it does not doCopy Anchor Link

It draws a simulated reaction, not an experiment. Assembly efficiency, the fidelity of a given overhang set at a given ligation temperature, and the frequency of misligation between similar overhangs are all real and none is modelled here — a plan that assembles cleanly on screen can still give you colonies with the wrong insert. It also draws the selected product only: a reaction that could produce several arrangements shows them one at a time.