Your workspace
Annotations
The coloured blocks on your map are labels somebody typed. They are worth keeping accurate, because everything downstream reads them.
A label is a claim, not a fact
This is the most important thing on this page. An annotation reading AmpR means somebody, at some point, drew a box there and typed “AmpR”. It does not mean the bases inside the box encode beta-lactamase. Files get edited, cassettes get swapped, boxes get left behind.
It matters because a wrong label propagates. If a feature is drawn over the wrong span, an edit anchored to that feature cuts in the wrong place. If a marker is mislabelled, a duplication check that counts by name will happily report one copy of something that is present twice.
Adding an annotation
Select the region on either map, right-click, and choose Edit Annotation. Or open the Annotation Palette from the toolbar and pick a feature type to apply to the current selection.
The palette is searchable — typing promoter, gene or primer narrows it quickly. Types are grouped:
| Category | What lives there |
|---|---|
| Regulatory Elements | Promoters, terminators, ribosome binding sites, operators, enhancers. |
| Genes & Expression | Coding sequences, open reading frames, tags, fusion domains. |
| Cloning & Assembly | Restriction sites, homology arms, overhangs, linkers, multiple cloning sites. |
| Selection Markers | Antibiotic resistance genes and other selectable markers. |
| Structural Elements | Origins of replication, scaffolds, structural repeats. |
| Custom Features | Anything your lab tracks that does not fit the standard vocabulary. |
Feature colours follow the conventions used by ApE, SnapGene and Benchling, so a map exported from GeneLoop looks like the maps your lab already reads. Types carry Sequence Ontology terms, which is what makes them survive the trip through GenBank into other software.
Correcting one
- Change the extent
- Select the correct span, right-click, and edit the annotation. Getting the boundaries right matters most for coding sequences, where a start position that is off by one or two bases puts the whole translation out of frame.
- Change the name or type
- Open the annotation and edit it in place. If you are relabelling because you discovered the bases are something else, say what they are rather than deleting the box — an unlabelled region is not more honest than a corrected one.
- Remove several at once
- Select a region and use Remove Annotations from the right-click menu. Remove Primers clears primer features specifically, which is useful after a design round leaves a dozen of them on the map.
Strand and direction
Draw features on the strand they are read from
A coding sequence on the bottom strand is read right to left. If it is annotated as forward, every translation you run against it comes back as nonsense, and it is very easy to conclude the construct is broken when the annotation is what is wrong.
Several standard expression vectors carry their cassette on the minus strand. If a construct looks full of internal stop codons, check the strand before you check anything else.
What survives an export
Annotations are written into GenBank output with their names, types, strands, colours and qualifiers, so a construct exported from GeneLoop opens with its map intact in other tools. FASTA carries none of it — FASTA has no way to express a feature.
File formats has the full picture of what survives which format.