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Bringing sequences in
Four ways to get DNA into a project: import a file, paste it, start from a stock vector, or ask the assistant to fetch a published deposit.
Import a file
Drag the file onto the Projects panel, or use + → Import File. The importer accepts:
| Extension | What it is |
|---|---|
.gb .gbk .gbff .genbank | GenBank. Carries sequence and annotations together — the format to prefer. |
.fa .fasta | FASTA. Sequence only, no features. |
.dna | SnapGene. |
.ape | ApE. |
.ab1 .scf | Sanger trace files from a sequencing run. |
.seq .txt | Plain text bases. |
Files up to 10 MB are accepted. Anything over 1 MB is given longer to parse, so a large genome-scale file may sit for a few seconds before it appears.
Paste a sequence
Use + → Paste Sequence for anything you have on the clipboard. Two settings matter, and getting them wrong is a common source of confusion later:
- Molecule type
- DNA, RNA or oligo. This decides how the sequence is displayed and which tools apply to it.
- Topology
- Circular or Linear. A plasmid is circular, and saying so matters: on a circular molecule, features can cross the origin and a digest produces a different fragment count. RNA and oligos are always linear.
Start from a stock vector
The paste dialog also carries a template picker with common backbones already annotated, so you do not have to source them:
| Vector | Category |
|---|---|
| pUC19 | Cloning |
| pBluescript II SK(+) | Cloning |
| pET-28a(+) | Bacterial expression |
| pGEX-4T-1 | Bacterial expression |
| pcDNA3.1(+) | Mammalian expression |
| lentiCRISPR v2 | Lentiviral / CRISPR |
| pEGFP-N1 | Fluorescent reporters |
These are the canonical sequences, not a copy of someone else's edited version — which is worth knowing, because a “pUC19” picked up from a colleague's folder has often had its lac promoter removed years ago and nobody renamed the file.
Ask the assistant to fetch one
If the construct you want is published, describing it in the chat is usually the fastest route. The assistant can pull sequences from Addgene, the iGEM Registry, UniProt, the PDB and NCBI, and it brings back the record with its accession attached so you can check it went to the right one.
Ask by identifier where you can
“Fetch Addgene #52961” resolves to exactly one thing. “Fetch lentiCRISPR v2” resolves to a family with many deposits, and you may get a different one than you had in mind. Where you have an accession or a catalogue number, give it.
Where the data comes from lists every repository it can reach and how to verify a record it hands you.
Check it before you build on it
Two minutes here saves a failed cloning round. Open the sequence and:
- Confirm the length
- The status bar shows total base pairs. Compare it against the published length. pUC19 is 2,686 bp; if yours says 2,655, something has been deleted from it.
- Confirm the topology
- The status bar says Circular or Linear. A plasmid imported as linear will give you wrong digest fragments and wrong coordinates across the origin.
- Look at the features
- Are the origin, the marker and the promoter drawn? A backbone with no features imported as sequence-only.