Sequence Viewer

The sequence viewer displays DNA sequences with annotations and interactive features.

Overview

The sequence viewer shows:

• Nucleotide sequence (A, T, G, C)

• Position markers

• Annotations as colored tracks

• Selection highlighting

Sequence Viewer

Navigating the Sequence

Scroll

• Use mouse wheel to scroll through the sequence

• Click and drag in the sequence area

Jump to Position

1. Click the position indicator in the status bar

2. Enter a position number

3. Press Enter to jump

Zoom

• Zoom in to see individual nucleotides

• Zoom out to see the full sequence overview

Selecting Sequence

Click and Drag

1. Click at the start position

2. Drag to the end position

3. Release to complete selection

Keyboard Selection

1. Click to position cursor

2. Hold Shift and use arrow keys

3. Or Shift-click at end position

Select All

Press Cmd/Ctrl + A to select the entire sequence.

Selection Information

When sequence is selected, the status bar shows:

• Start: Beginning position

• End: Ending position

• Selection: Number of bases selected

• GC%: GC content of selection

• Melting temp: Estimated Tm

Working with Selections

Copy Selection

1. Select sequence

2. Press Cmd/Ctrl + C

3. Paste as nucleotide text

Copy Options

Right-click selection for options:

• Copy sequence: Nucleotide sequence

• Copy reverse complement: Reverse complement

• Copy amino acid translation: Translated sequence (for CDS regions)

Create Annotation

1. Select sequence

2. Right-click > Create annotation

3. Fill in annotation details

4. Click Create

Create Part

1. Select sequence

2. Right-click > Create part from selection

3. Enter part details

4. Save to your parts library

Annotations Track

Annotations appear below the sequence:

Viewing Annotations

• Colored bars indicate annotated regions

• Labels show annotation names

• Click an annotation to select it

Annotation Details

Click an annotation to see:

• Name and type

• Position (start, end)

• Direction (forward/reverse)

• Additional properties

Managing Visibility

1. Click View menu

2. Select annotation types to show/hide

3. Simplify view for complex constructs

Sequence Display Options

Translation

Show amino acid translation:

1. Select a CDS annotation or region

2. Translation appears above/below sequence

3. View reading frame

Complement Strand

Toggle complement strand display:

• Shows both strands

• Useful for primer design

• Toggle in View menu

ORF Highlighting

Highlight open reading frames:

1. View > Show ORFs

2. ORFs highlighted in sequence

3. Click to see ORF details

Status Bar

The bottom status bar shows:

• Current position

• Construct length (bp)

• Selection range

• GC content

• Melting temperature

Keyboard Shortcuts

Shortcut	Action
Arrow keys	Move cursor
Shift + Arrow	Extend selection
Cmd/Ctrl + A	Select all
Cmd/Ctrl + C	Copy
Cmd/Ctrl + F	Find in sequence
Home	Go to start
End	Go to end

Next Steps

• Codon Optimization — Optimize sequences

• Sequence Analysis — Analyze properties

• Annotations — Label features