Manage Enzymes

Choose which restriction enzymes the editor shows you — the enzymes you own, the ones hidden by default, and custom groups you build for a particular job.

What it doesCopy Anchor Link

A plasmid map that draws every known restriction site is unreadable, and most of those sites are for enzymes you cannot buy and would never use. This is where you decide what the editor shows.

Enzymes are organised into groups, and a group is a display filter: putting an enzyme in a group makes it available in the cut-site filter, on the map and in the tools that cut. It does not change anything about the enzyme itself — its recognition sequence, its cut offsets and its overhang are properties of the enzyme, not of your list.

Two groups always exist:

• My Enzymes — the working set, and where custom enzymes you define yourself live.
• Hidden — the less common enzymes, kept out of the way by default. They are still fully described and fully usable; adding one to a group is what makes it appear in the cut-site filter.

Everything else is a group you make. Type a name, copy enzymes into it from any other group, and you have a list you can switch to — the enzymes your lab stocks, the six you are screening a construct with, the Type IIS set you assemble with.

When you'd use thisCopy Anchor Link

• Once, when you start, to make My Enzymes match what is actually in your freezer. Every map you read afterwards is cleaner for it.
• Before a diagnostic digest, to build a group of the enzymes you are considering, so the map shows those sites and nothing else.
• When an enzyme you want is not offered. It is almost certainly in Hidden rather than missing — search for it and copy it into a group.
• When you work with an enzyme the catalogue does not carry — a new isoschizomer, an engineered variant, an enzyme from a supplier we do not track — define it as a custom enzyme.

What this computesCopy Anchor Link

• The groups themselves — which enzymes the rest of the editor offers you
• A search that accepts a name or a number of cuts, so "which enzymes cut this sequence exactly once" is a search rather than a study
• A hover preview of any enzyme's details, so a recognition site can be checked without leaving the list
• Custom enzymes you define, alongside the catalogue
• What a group does to the molecule you have open — a reading of the whole group against the sequence, rather than a list you count by hand: how many of its enzymes were resolved against the catalogue and how many were not recognised at all, the total number of cuts, and the group split into single cutters, double cutters, enzymes cutting three times or more and enzymes that do not cut this molecule. A single cutter is what linearises a plasmid, so that count is usually the reason you opened the group
• An enzyme the catalogue does not carry is reported as unrecognised, never as zero cuts. They are opposite answers: this enzyme does not cut here is a result about your molecule, and this name is not in the catalogue is a result about your list, and a group that quietly reads a typo as a non-cutter would tell you a screen is clean when it was never run
• Circular and linear are scanned differently — a site spanning the origin exists on a plasmid and does not exist on the same sequence read as linear, so the reading states which it used

Where it livesCopy Anchor Link

Manage Enzymes, opened from the Tools menu and from the cut-site filter, docked in the right rail. Group membership is remembered between sessions and applies across the workbench: the cut-site filter, the sequence and circular maps, the digest tool and the cloning tools all read the same groups, so there is one answer to "which enzymes am I working with" rather than one per surface.

Inputs and outputsCopy Anchor Link

In: the enzyme catalogue, plus any custom enzymes you define.

Out: the groups themselves — which enzymes the rest of the editor offers you.

Searching accepts a name or a number of cuts, so "how many enzymes cut this sequence exactly once" is a search rather than a study. Hovering an enzyme previews its details, so you can check a recognition site without leaving the list.

ControlsCopy Anchor Link

The scienceCopy Anchor Link

The catalogue is REBASE, the restriction-enzyme database maintained by New England Biolabs — the authority for recognition sequences, cut positions and isoschizomer relationships. Each record carries its recognition site, its cut offsets on both strands (which is what determines whether it leaves a 5′ overhang, a 3′ overhang or a blunt end), and its aliases, so an enzyme found under any of its names is the same record.

Type IIS enzymes, which cut at a distance from their recognition site rather than inside it, are identified from their cut geometry rather than from a declared flag — a label and the offsets beside it can disagree, and when they do the offsets are what the enzyme actually does.

Cut sites drawn on the map, cut positions used by the digest tool and the overhangs used by the cloning tools all come from that same dataset, checked against REBASE, so a site you can see is a site the tools will cut at.

LimitationsCopy Anchor Link

• Groups are display filters, not scientific claims. Hiding an enzyme does not mean it will not cut your sequence; it means you have asked not to be shown it. Before concluding a sequence has no site for something, check that the enzyme is in the group you are viewing.
• Custom enzymes are yours. An enzyme you define is not checked against any authority, because there is nothing to check it against — you are asserting its recognition sequence and its cut positions, and the tools will believe you.
• Groups are stored per browser. They travel with the browser you set them up in, not with the project or the account.
• The group reading counts CUT SITES, not fragments. One site on a circular plasmid gives one linear product; one site on a linear molecule gives two. The number of bands you expect on a gel follows from the sites and the topology together, and the digest tool is where that is worked out.
• Star activity, methylation sensitivity and buffer compatibility are not modelled. Whether an enzyme will actually cut your DNA in your buffer, and whether a Dam or Dcm site blocks it, are properties of the reaction that a site list cannot answer.

RelatedCopy Anchor Link

In this group: Edit annotation · Enzyme · Insert sequence · Merge features · Dot plot · Dot plot grid · Melt curve · Amplification curves · Population genetics · RNA-seq · Site avoidance heat map · Protein coverage · Reference-gene stability · Digital PCR · Codon usage matrix · Pairwise distance distribution · Nearest-neighbor distances · GC content distribution · Base composition per cycle · Pairwise distance grid · Per-cycle channel occupancy · Grammar assembly plan · Gibson assembly plan · Assembly plan build order · Golden Gate assembly plan · Guide track · Primer binding track · Hydropathy profile · Charge vs pH · Amino-acid composition · Hydrophobic moment · Optimization profiles · Digest gel · Virtual gel · Initiation-window fold · Antibody domain map · Electropherogram · Circuit netlist · Circuit transfer functions · Circuit construct · Construction graph · Protocol · Read Quality Profile · Read Alignment · Raw Signal · Verify vs Reference · Chromosomal microarray · Variant calls · Small molecule