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Navigation

Mauve Viewer provides several ways to explore genome alignments: zooming, panning, a cross-track cursor, region selection, and a feature search interface.

Zooming

You can zoom in and out to view the alignment at different scales, from a full-genome overview down to individual nucleotide positions.

Action Effect
Ctrl + Up Zoom in 2x
Ctrl + Down Zoom out 2x
Ctrl + Scroll wheel Zoom in or out at the mouse position
Toolbar zoom buttons Zoom in or out 2x

The zoom range spans from 1x (full overview) to 100,000x (nucleotide level).

Panning

Move the visible region left or right along the genome.

Action Effect
Drag Pan by dragging directly on the alignment
Ctrl + Left Scroll left by 10% of the visible region
Ctrl + Right Scroll right by 10% of the visible region
Ctrl + Shift + Left Scroll left by 20% of the visible region
Ctrl + Shift + Right Scroll right by 20% of the visible region
Toolbar pan buttons Scroll left or right

Cross-Track Cursor

When you hover over a genome panel, a black vertical bar appears at the cursor position. Corresponding vertical bars appear at the homologous positions in all other visible genomes. This lets you visually track how a position in one genome maps to the others through the alignment.

The information display shows:

  • Genome name
  • Nucleotide position
  • LCB details (if hovering over a block)

When you hover over an LCB block, it is highlighted with a thicker stroke and higher opacity.

Centering on Homologous Sites

Click on any position in a genome panel to smoothly center all panels on the corresponding homologous positions. The centering animation takes 300 milliseconds.

Region Selection

You can select a rectangular region for visual highlighting.

  1. Hold Shift and drag across a genome panel (minimum 5 pixels).
  2. A solid-bordered highlight rectangle appears on the source panel.
  3. Dashed-bordered rectangles appear on other panels at the corresponding homologous regions.

To clear the selection:

  • Shift + click without dragging (less than 5 pixels of movement), or
  • Press Escape.

The selection is purely visual and does not trigger automatic zooming.

Sequence Navigator

Press Ctrl + G to open the Sequence Navigator. This panel is only available when annotation files are loaded alongside the alignment.

Find Features Tab

Search for genomic features by entering a query term and selecting search criteria.

Search fields:

  • locus_tag
  • gene
  • product
  • protein_id
  • note
  • db_xref

Search modes:

  • Exact — Matches the full field value (case-insensitive)
  • Contains — Matches any substring (case-insensitive)

Scope:

  • All genomes (default)
  • A specific genome

Results display up to 100 matches. Each result shows the feature type, genome, locus_tag, gene name, product, coordinates, and strand. If more than 100 matches exist, the overflow count is displayed.

Click a result to navigate the viewer to that feature's position.

Go To Position Tab

Jump directly to a specific nucleotide coordinate.

  1. Select a genome from the dropdown.
  2. Enter a position number.
  3. Press Enter or click the Go button.

Invalid or non-positive positions are rejected with an error message.