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Getting started

The minimum you need to know to be productive on day one.

Launch

splicecraft                       # empty canvas
splicecraft L09137                # fetch pUC19 from NCBI on launch
splicecraft myplasmid.gb          # local GenBank
splicecraft mything.dna           # popular commercial plasmid editor format

Press ? once running for the full keyboard-shortcut reference, rendered as a Markdown modal so you can drag-select a combo to copy.

First five seconds with pUC19

splicecraft L09137

What you should see:

  • Circular braille map in the centre — pUC19 ring with feature arcs in distinct colours.
  • Feature sidebar on the right listing CDS, primer_bind, and rep_origin features.
  • Library panel on the left (empty until you add this plasmid via Alt+K).
  • Sequence panel at the bottom, two-strand, with the cursor at bp 1.

Try these in order:

  1. r — toggle restriction-site overlay. Watch BamHI, HindIII, EcoRI, and others light up on the map and sequence panel.
  2. Click on the EcoRI site — upstream bases tint blue, downstream red, with the staggered overhang flipped between strands.
  3. v — toggle linear view. +/- zoom; [/] pan; 0 reset.
  4. Enter on the sequence panel — highlight the feature enclosing the cursor.
  5. Ctrl+A, Ctrl+C — select all + copy the top strand.
  6. Alt+C — copy the reverse complement instead.
  7. Alt+K — add ("keep") pUC19 in the library.
  8. Ctrl+Q — quit. Re-launch with splicecraft; pUC19 is in the panel.

Three workflows that motivate the design

"I'm planning a cloning."

Constructor → Traditional or Constructor → Gibson or Constructor → Golden Braid. Pick your insert source (current plasmid / library entry / free-form PCR product / Parts Bin), pick your vector, simulate the digest + ligation. Save the product back to the library with full construction-history XML preserved for downstream auditability.

See Features → Cloning.

"I need diagnostic primers for this region."

Ctrl+P opens the Primer Design workbench. Choose detection / cloning / Golden Braid / generic, pick the target region, click Design. Primer3 returns ranked candidates; promote them to primer_bind features on the map or save to the persistent primer library (Designed → Ordered → Validated lifecycle).

See Features → Primer design.

"I have a .dna archive from the previous PI."

File → Bulk import folder…, point at the archive, give the collection a name. Every .dna / .gb / .gbk file inside is loaded independently; failures per file are isolated and surfaced in a notify summary. The popular commercial plasmid editor's construction-history XML is preserved on import and re-emitted on save — so the lineage of a multi-step build survives the round-trip.

See Features → Library.

Where to go next