Your workspace
The sequence workspace
Open a sequence and you get two views of the same molecule, a selection that every tool understands, and a status bar that tells you what you are actually looking at.
Two views of one molecule
Every sequence opens with two tabs. They are the same DNA — switching does not change anything, only how you see it.
- Plasmid Map
- The circular view. Best for taking in the whole construct at once: where the origin sits relative to the marker, whether your insert landed where you meant it to, how much of the plasmid a cassette occupies.
- Linear Map
- The unrolled view. Best for anything positional — junctions, spacing between a ribosome binding site and a start codon, reading along a cassette in order.
Read the status bar first
The strip along the bottom is the most useful thing on screen and the most ignored. It shows, left to right:
- Total length in base pairs — check this against the published length of whatever you imported.
- Circular or Linear — a plasmid marked linear will give you the wrong fragment count on a digest and wrong coordinates across the origin.
- Feature count — a backbone showing zero features came in as a bare sequence.
- The current selection, as start–end and a length.
- The sequence name.
Selecting a region
Drag on either map to select. The selection is shared by everything else: design primers for it, search it for cut sites, translate it, send it to the assistant, or paste over it.
Select more than about ten bases and an insights panel appears with instant properties of that region and shortcuts to act on it — design primers, find sites, ask the assistant. It is the quickest way to answer “what is this bit?” without opening a tool.
The right-click menu
Right-clicking a selection is where most of the work happens. Grouped by what they are for:
| Group | Items |
|---|---|
| Hand it off | Send to AI Assistant · Document in Lab Notebook |
| Read it | Show Amino Acids · Translate (choose frame, strand and genetic code) |
| Annotate it | Edit Annotation · Remove Annotations · Remove Primers |
| Analyse it | PCR Simulation · Digest Simulation · Primer Design · Enzyme Search · BLAST Search · Cloning Planner |
Tabs and windows
Sequences, documents, experiments, protocols and diffs all open as tabs in the same bar. Drag to reorder them; double-click the name to rename in place.
Because a diff is a tab like any other, you can leave a comparison open next to the construct while you keep working — useful when you are checking a build against what you intended.
Editing by hand
You can edit directly: select, type or paste, and the map redraws. Pasting a large fragment asks you to confirm what you are about to do first.
| Action | Key |
|---|---|
| Undo | ⌘Z |
| Redo | ⌘⇧Z |
| Copy selection | ⌘C |
| Paste | ⌘V |
| Close the tool drawer | Esc |
What is not in this view
Two things people look for here live elsewhere. There is no standalone ORF-finder panel — use Translate with an explicit frame, or ask the assistant to sweep the construct for open reading frames. Codon usage and adaptation index are likewise not a panel; ask for them in the chat.
If you are browsing as a guest
All nine analysis tools, export and version history are disabled until you sign up. You can look at a sequence and move around it, but you cannot analyse, change or save one.