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Dotplot view

The dotplot view is a 2D comparative view that can display alignments between different genome assemblies, or even compare a long-read or NGS short-read against the genome.

Opening a dotplot view​

  1. Navigate on the header bar Add->Dotplot view
  2. Select the genome assemblies of interest
  3. Optionally, add a .paf, .out (MashMap), .delta (Mummer), .chain, .anchors or .anchors.simple (MCScan) file
Adding a new dotplot or synteny view via the menubar.
Adding a new dotplot or synteny view via the menubar.
Screenshot of the import form for a dotplot or synteny view. You can select two different assemblies and an additional file can be supplied.
Screenshot of the import form for a dotplot or synteny view. You can select two different assemblies and an additional file can be supplied.
Screenshot of a dotplot visualization of the grape vs the peach genome.
Screenshot of a dotplot visualization of the grape vs the peach genome.
Screenshot showing the linear synteny view for the grape vs peach genome.
Screenshot showing the linear synteny view for the grape vs peach genome.

Opening a synteny view from a dotplot view​

You can open a synteny view from a dotplot view by selecting a region on the dotplot and clicking "Open linear synteny view", shown below:

Screenshow showing the 'click and drag' selection over the dotplot view which prompts you to open up a linear synteny view from the selected region.
Screenshow showing the 'click and drag' selection over the dotplot view which prompts you to open up a linear synteny view from the selected region.