Merge Features
Join two annotations into one that spans from the start of the first to the end of the second, keeping or removing the originals.
What it does
Pick two features, give the result a name, and it creates one feature running from the start of Feature 1 to the end of Feature 2. The originals are removed by default, or kept if you say so.
That directionality is the thing to understand before you use it: the merged feature is not "the union of both" or "the span they cover" — it is from the first one's start to the second one's end, in the order you put them in. If you choose them the wrong way round you get a feature running the other way, which is what the Swap control is for. The new start and end are shown before you commit, so you can see what you are about to make.
The merged feature inherits Feature 1's properties — its type, its strand, its colour — with your new name and the new bounds.
When you'd use this
- Repairing a split annotation. An imported record where one gene arrived as two adjacent features, or an auto-annotation run that found a promoter as two overlapping hits.
- Making one region out of two abutting parts — a promoter and its 5′ UTR, two exons you want to treat as one block, a tag and the linker in front of it.
- Building a feature that spans a gap deliberately, where the region between the two features should be inside the annotation rather than outside it.
What this computes
- One new feature spanning from Feature 1's start to Feature 2's end, left selected on the map so you can see what was made
- The two originals removed, unless you asked to keep them
What it refuses: committing without both features chosen and without a name — each is required and says so, rather than producing a nameless feature or a partial merge. A feature already chosen in one dropdown is removed from the other's options, so a feature cannot be merged with itself.
Where it lives
Merge Features, from the annotation right-click menu and the Tools menu, docked in the right rail. It reads the live document, so the dropdowns list the open sequence's real features.
Choosing features works two ways, and the panel says so: pick them in the dropdowns, or shift-click the features directly on the plasmid map. The selection and the panel are the same state — clicking on the map fills the dropdowns.
Inputs and outputs
In: two features on the open sequence, and a name. If you already had features selected when you opened the panel, they are pre-filled.
Out: one new feature, from Feature 1's start to Feature 2's end, and — unless you asked to keep them — the two originals removed. The new feature is left selected on the map, so you can see what was made.
What it refuses: committing without both features chosen and without a name. Each is required and says so, rather than producing a nameless feature or a partial merge. A feature already chosen in one dropdown is removed from the other's options, so you cannot merge a feature with itself.
Controls
| Control | What it does |
|---|---|
| Feature 1 | The feature whose start the merged feature begins at, and whose properties it inherits. |
| Feature 2 | The feature whose end the merged feature finishes at. |
| Swap | Exchanges the two, which is the fix when the bounds preview is not what you meant. |
| Use name (beside each) | Copies that feature's name into the New Name field. |
| New Name | The merged feature's name. Required. |
| New Start / New End | The resulting bounds, shown as they will be applied — derived from your two choices rather than typed. |
| Preserve features | Off by default: the two originals are removed once merged. Turn it on to keep them alongside the new one. |
| Create merged feature | Commits. |
The science
There is no biology in the operation itself, but there is a convention worth stating: the merge is ordered, not set-like. From Feature 1's start to Feature 2's end is a different span from the union of the two features whenever they do not overlap, and a different span again from Feature 2's start to Feature 1's end. That is deliberate — it is what lets you deliberately include the gap between two features — and it is why the bounds are shown before you commit.
The whole operation is one undo step, including the removal of the originals, so an accidental merge is one keystroke away from being undone rather than three.
Coordinates shown are 1-based inclusive, matching the sequence ruler and the rest of the editor.
Limitations
- Two features at a time. Merging three is two merges.
- The result inherits Feature 1, so if the two differ in type or strand, Feature 2's properties are not carried over. Check the type on the result if the two were not alike.
- No warning when the features are far apart. Merging two features at opposite ends of a plasmid is a legitimate operation and produces a feature covering nearly everything between them; the bounds preview is your check, and there is no second one.
- Removal is real. With Preserve features off, the originals are deleted — recoverable by undo, but not by re-opening the panel.
Related
In this group: Edit annotation · Enzyme · Insert sequence · Manage enzymes · Dot plot · Dot plot grid · Melt curve · Amplification curves · Population genetics · RNA-seq · Site avoidance heat map · Protein coverage · Reference-gene stability · Digital PCR · Codon usage matrix · Pairwise distance distribution · Nearest-neighbor distances · GC content distribution · Base composition per cycle · Pairwise distance grid · Per-cycle channel occupancy · Grammar assembly plan · Gibson assembly plan · Assembly plan build order · Golden Gate assembly plan · Guide track · Primer binding track · Hydropathy profile · Charge vs pH · Amino-acid composition · Hydrophobic moment · Optimization profiles · Digest gel · Virtual gel · Initiation-window fold · Antibody domain map · Electropherogram · Circuit netlist · Circuit transfer functions · Circuit construct · Construction graph · Protocol · Read Quality Profile · Read Alignment · Raw Signal · Verify vs Reference · Chromosomal microarray · Variant calls · Small molecule
Insert sequence
Type bases or residues into the sequence at the caret, or replace what you have selected — with live cleaning of what you type and no silent loss of it.
Manage Enzymes
Choose which restriction enzymes the editor shows you — the enzymes you own, the ones hidden by default, and custom groups you build for a particular job.