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Quickstart: your first document

A tour of the workspace, then a full path from import to cloning: import a plasmid > read its annotations > make your first cloning product.

5 min read

The workspace at a glance

deoxy is a single browser workspace with four regions. You will use all of them in this guide.

Nav rail
The vertical icon column on the far left. The + button creates and imports documents. The gear opens Settings.
Sidebar
Your document list. Filter, sort, search, and organize by label. Click any card to open it in the editor pane.
Editor pane
The open document. Its toolbars hold zoom, the Layers dropdown, and per-doctype actions (cloning workflows, align, map, BLAST, etc.).
Bottom panel
Tabbed drawers for Linear maps, Annotations, Primers, Restriction sites, Labels, and more.

Import a plasmid

We will pull a well-known plasmid straight from NCBI by accession, no file needed.

  1. Open the Import modalClick + in the nav rail, then Import.
  2. Switch to the accession laneChoose By accession, leave the source on Auto-detect, and enter an accession such as J01749 (the pBR322 plasmid).
  3. Look it upClick Look up. A preview card shows the accession, title, organism, and length so you can confirm before importing.
  4. Set topology and importFor a plasmid, set Topology to Circular (GenBank records that declare topology set this for you), then click Import.

The document opens in the editor with its features already annotated. Anything over 100,000 bp is offered as a streamed genome document instead. See the Importing guide for how that routing works.

Read what you imported

Take a moment to explore before editing.

  1. Open the circular mapClick Show circular view in the toolbar to see the plasmid as a ring with its features placed around it.
  2. Browse featuresOpen the bottom panel and select the Annotations tab to see every feature, its coordinates, and type. Clicking a row highlights it in the editor.
  3. Check the statsThe Metadata tab shows length, melting temperature, molecular weight, and base composition, plus a translation block for each CDS.

Make your first cloning product

Now do something only a sequence tool can: cut and paste DNA correctly.

  1. Find a cut siteOpen the Restriction sites tab. Use the filter menu to pick the Common cloners enzyme set, then find a single-cutter such as EcoRI.
  2. Start restriction cloningOpen the toolbar Cloning workflows dropdown and choose Restriction cloning. The open document becomes the backbone.
  3. Pick enzymes and an insertChoose Enzyme 1 (and optionally Enzyme 2), then set the Insert source to a document or pasted sequence. deoxy previews the junction overhangs and product length live.
  4. Create the documentClick Create document. The product opens as a brand-new document with full cloning provenance recorded, so you can always see how it was built.

Where to go next

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