Dotplot view

The dotplot view is a 2D comparative view that displays alignments between genome assemblies, or between a single read and the genome. Syntenic regions appear as diagonal lines or blocks; inversions appear as reverse-diagonal segments; translocations and rearrangements appear as off-diagonal blocks.

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.
Dotplot of grape (Y-axis) vs peach (X-axis) genomes. Diagonal streaks are syntenic blocks where the two genomes are collinear. Off-diagonal blocks indicate chromosomal rearrangements; reverse-diagonal segments indicate inversions.
Dotplot of grape (Y-axis) vs peach (X-axis) genomes. Diagonal streaks are syntenic blocks where the two genomes are collinear. Off-diagonal blocks indicate chromosomal rearrangements; reverse-diagonal segments indicate inversions.
Linear synteny view of the grape vs peach genome generated from the same PAF file as the dotplot. Colored ribbons connect collinear blocks between the two assemblies — red ribbons are forward-strand alignments, blue are inverted. The alignment depth and extent of synteny are clearer at this scale than in the dotplot.
Linear synteny view of the grape vs peach genome generated from the same PAF file as the dotplot. Colored ribbons connect collinear blocks between the two assemblies — red ribbons are forward-strand alignments, blue are inverted. The alignment depth and extent of synteny are clearer at this scale than in the dotplot.

Opening a synteny view from a dotplot view

Click and drag to select a region in the dotplot, then choose Open linear synteny view from the context menu. This zooms into that region in a new linear synteny view with both genomes shown as tracks.

Top: click-and-drag selection (pink highlight) on the grape vs peach dotplot, with the context menu showing 'Zoom in' and 'Open linear synteny view'. Bottom: the resulting linear synteny view for the selected region (Pp02 vs chr15), with red connection lines linking each syntenic alignment block across the two genome panels.
Top: click-and-drag selection (pink highlight) on the grape vs peach dotplot, with the context menu showing 'Zoom in' and 'Open linear synteny view'. Bottom: the resulting linear synteny view for the selected region (Pp02 vs chr15), with red connection lines linking each syntenic alignment block across the two genome panels.

For a step-by-step walkthrough of loading assemblies, generating a PAF with minimap2, and using the dotplot and linear synteny views together, see the Synteny and genome alignment tutorial.