Annotations
Annotations label features and regions within your construct sequence.
What Are Annotations?
Annotations are simple labels that mark specific sequence regions. They document features within your construct but are not designed for reuse across designs. Each annotation has:
Name: Feature identifier
Type: Category label (CDS, misc_feature, etc.)
Location: Start and end positions
Direction: Forward or reverse strand
Additional properties: Color, notes, qualifiers
Annotations vs. Parts
Simple annotations are lightweight labels:
Exist only within one construct
Good for documenting features from imported files
Not searchable as standalone items
Not intended for reuse
Parts are reusable genetic elements:
Have their own file and identity
Searchable across your workspace
Designed for reuse in multiple constructs
Contain rich metadata
If you have a genetic element you want to reuse (a promoter, gene, terminator, etc.), create it as a part rather than just annotating it. See Creating Parts.
Creating Annotations
From Selection
In the sequence viewer, select a region by clicking and dragging
Right-click the selection
Select Create annotation
Enter:
Name
Type (CDS, promoter, misc_feature, etc.)
Strand direction
Click Create
From Parts
When you add a part to a construct:
A part annotation is automatically created
Links the sequence region to the part definition
Import with File
GenBank files include annotations:
Annotations import automatically
Review and edit imported annotations
Optionally link to existing parts
Editing Annotations
Change Properties
Click an annotation in the sequence viewer
The annotation details panel opens
Edit name, type, or other properties
Changes save automatically
Resize Annotation
Select the annotation
Drag the edges to resize
Or edit start/end positions in the properties panel
Move Annotation
Select the annotation
Drag to a new location
Or update the position values
Delete Annotation
Select the annotation
Press Delete or right-click and select Delete annotation
Annotation Visualization
Sequence Viewer
Annotations appear as:
Colored bars below the sequence
Labels showing annotation name
Arrows indicating direction
Schematic View
Part annotations show as:
Symbols in the schematic
Names angled above
Color-coded by type
Circular Map
On circular constructs:
Annotations display around the circle
Color and labels match other views
Annotation Types
Common annotation types:
CDS
Coding sequence (gene)
promoter
Transcription promoter
terminator
Transcription terminator
rep_origin
Replication origin
misc_feature
General feature
primer_bind
Primer binding site
protein_bind
Protein binding site
regulatory
Regulatory element
Managing Multiple Annotations
Overlapping Annotations
Annotations can overlap:
Common for nested features
Displayed in stacked tracks
Each maintains independent properties
Bulk Operations
Select multiple annotations:
Shift-click: Select range
Cmd/Ctrl-click: Add to selection
Apply changes to all selected
Hide/Show Annotations
Control annotation visibility:
Click View menu
Select Annotation visibility
Toggle types on/off
Simplify the view for complex constructs
Linking to Parts
Convert Annotation to Part
Select a simple annotation
Right-click and select Create part from annotation
Fill in part details
The annotation becomes a part annotation
Link Existing Part
Select an annotation
In properties, click Link to part
Search and select a part
The annotation references that part
Best Practices
Naming
Use clear, descriptive names
Follow conventions (e.g., GenBank standard names)
Be consistent across constructs
Organization
Annotate all functional regions
Use appropriate types
Include notes for complex features
Maintenance
Update annotations when sequences change
Link annotations to parts for reusability
Review imported annotations for accuracy
Next Steps
What is a Construct? — Construct overview
Creating Parts — Build reusable parts from annotations
Sequence Viewer — Working with sequences
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