Restriction digest
The restriction digest tools find where enzymes cut your sequence, what overhangs they leave, and what fragment sizes you would see on a gel.
What a digest tells you
A restriction enzyme recognizes a short, specific sequence of DNA and cuts the double helix at or near that site. Knowing where an enzyme cuts a plasmid, and how many times, is the everyday question behind picking cloning sites, designing a diagnostic digest, and reading a gel. The restriction digest tools in the Sequences workbench answer that question for any DNA sequence you have open. They tell you which enzymes cut, at what positions, on which strand, what overhang each cut leaves, and what fragment sizes result.
The digest is a display layer on the open sequence. Turn on the Enzyme sites chip in the display strip above the viewer to overlay cut sites on the circular or linear map, and open the enzyme picker (the Choose enzymes action under the Cut operation in the right sidebar) to choose which enzymes are active. The digest overlay itself saves nothing. The active enzyme set lives in the editor's view state for the session, though you can name and keep a set of your own from the picker (see below).
Watch the app demos→The enzyme catalog
The Workspace ships with a catalog of 236 restriction enzymes drawn from a standard NEB-derived dataset. Each enzyme carries its recognition sequence and its cut geometry, and from that the catalog derives the metadata you filter on. That covers how long the recognition site is, whether the site is palindromic, whether it contains a degenerate (non-ACGT) code, and what overhang the cut leaves. You never have to type an enzyme's recognition site or cut position, it all comes from the bundled data.
Cut detection on both strands
For a given sequence and enzyme set, the digest searches the recognition site on both strands, the forward strand and the reverse complement, so a cut site is found regardless of which way the recognition sequence reads. Each cut records its position and which strand the recognition site sat on. The result is a per-enzyme breakdown that lists every enzyme in the active set, each place it cuts, and a total cut count. That count is what drives the unique-cutter and N-cutter filters described below.
Overhangs, 5 prime, 3 prime, and blunt
When an enzyme cuts, the top-strand cut and the bottom-strand cut may land at the same position or at offset positions. When they coincide, the cut leaves a blunt end. When the top strand cuts before the bottom strand, the cut leaves a 5' overhang. When the top strand cuts after, it leaves a 3' overhang. The catalog labels each enzyme's overhang type, so you can pick for the geometry your downstream ligation needs (compatible sticky ends, or blunt ends for a blunt ligation). This is the same overhang typing the Cloning Workspace uses when it ligates pieces, so a cut you reason about here behaves the same way in an assembly.
Fragment sizes and topology
Once the cut positions are known, the digest computes the fragment sizes you would see on a gel, sorted from largest to smallest. Topology matters here. For a linear molecule the two ends are open, so the cuts divide it into fragments with a piece at each end. For a circular molecule the fragments wrap around the origin, and a cut that spans the origin is handled correctly rather than splitting the molecule at an artificial seam. A sequence with no cuts reports a single fragment of the full length, which is the honest answer for a non-cutter.
Filters and enzyme sets
The enzyme picker mirrors the SnapGene chooser. You can search enzymes by name, hide enzymes that never cut the open sequence, and restrict the list by cut-count category. You can show only the enzymes that cut exactly once (unique cutters), or those that cut exactly N times, or the non-cutters. You can also require a minimum recognition-site length (longer sites cut more rarely and more cleanly), restrict to palindromic sites only, restrict to non-degenerate ACGT sites only, and restrict to a single overhang type.
Alongside the manual filters, a few computed presets give you a one-click set that is always derived from the current sequence. Common is the everyday workhorse set (EcoRI, BamHI, HindIII, and friends) intersected with the enzymes that actually cut this molecule. Unique cutters is every enzyme that cuts exactly once. The six-plus preset is every cutter whose recognition site is six bases or longer. All cutters is every bundled enzyme that cuts this sequence at least once. Because the presets are recomputed from the open sequence, Unique cutters really means unique on this molecule, not unique in general.
When you settle on a selection you want to reuse, the Saved sets control lets you name it and keep it. Saved sets are stored per user in a small sidecar file (users/<you>/_enzyme_sets.json) and follow you across every sequence you open. They are not shared with labmates, so each user builds their own panel of go-to sets. A saved set is one click away the next time, not something you rebuild by hand.
From a digest to a clone
The restriction digest and the Cloning Workspace are two views of the same enzyme model. Use the digest to find the cutters and overhangs you want, then carry the same enzymes into a restriction-ligation or Golden Gate assembly in the Cloning Workspace to build the construct. Because both share the bundled enzyme dataset and the same cut geometry, what you see in the digest is what the assembly does.