Reference
File formats
GenBank is the format that carries everything. This page is the detail of what the others keep and what they drop.
What GeneLoop reads
| Extension | Format | Brings features in? |
|---|---|---|
.gb .gbk .gbff .genbank | GenBank | Yes — the recommended format for anything annotated. |
.fa .fasta | FASTA | No. Sequence only. |
.dna | SnapGene | Yes. |
.ape | ApE | Yes. |
.ab1 .scf | Sanger traces | No. Base calls from a read. |
.seq .txt | Plain text | No. |
Files are accepted up to 10 MB. Files over about 1 MB are given longer to parse, so a large one may take a few seconds to appear.
What GeneLoop writes
| Format | Extension | Contents |
|---|---|---|
| GenBank | .gb | Sequence, all features, strands, colours, qualifiers. The complete record. |
| FASTA | .fasta | Header line and bases. |
| SnapGene | .dna | GenBank-format text with a .dna extension — see below. |
| SBOL | .xml | A minimal SBOL 2 record: one component definition and its sequence. |
| Plain text | .txt | Bases only. |
| JSON | .json | The full record in a machine-readable form, for scripting. |
The GenBank round trip
Export a construct from GeneLoop, import it again, and this is what comes back intact:
- Features
- Names, types, coordinates, strands and qualifiers.
- Colours
- Written in the convention ApE and SnapGene use, so your map looks the same in all three.
- Features that cross the origin
- A feature wrapping the start of a circular plasmid is written as a compound location and read back correctly — not silently truncated at the origin.
- Primers and translations
- Carried in a structured comment block, so a construct you have designed primers against does not lose them on export.
Coordinates
What the numbers mean
Positions shown in the interface and in exported GenBank are 1-based and inclusive — the same convention GenBank, SnapGene and ApE use. A feature spanning bases 100 to 150 includes both base 100 and base 150, and is 51 bases long.
On a circular plasmid, a feature can end at a lower number than it starts. That is not an error; it is a feature that crosses the origin.
Choosing one
| Sending it to | Use |
|---|---|
| A colleague, or your own records | GenBank |
| A synthesis vendor | FASTA for the order, GenBank for your file |
| BLAST or an aligner | FASTA |
| SnapGene | GenBank, or the .dna export |
| A script you are writing | JSON |
| A parts repository | SBOL |
When in doubt, GenBank. It is the only one that loses nothing, and everything reads it. Exporting and sharing.
When an import looks wrong
- No features on the map
- The file came in as FASTA or plain text. Re-export it as GenBank from wherever it came from.
- The wrong length
- Compare against the published length. A plasmid that is short by a few hundred bases has had something removed — check the features before you build on it.
- Drawn as linear when it is a plasmid
- Some formats carry no topology. Set it to Circular, or digests and coordinates across the origin will be wrong.
- Features in the wrong place
- Almost always an off-by-one from a tool using a different coordinate convention. Check one feature against the source record and, if it is shifted, it will be shifted the same way throughout.