Circular Genome Viewer

Overview

The Circular Genome Viewer provides a circular interactive graphical representation of the alignment of genes and other genomic data.

Accessing the Circular Genome Viewer on the PATRIC Website

Clicking the Circular Viewer tab in a Genome View displays the interactive Circular Genome Viewer, shown below.

../../_images/circular_viewer.pngCircular Genome Viewer

The Circular Genome Viewer provides a circular interactive graphical representation of the alignment of genes and other genomic data. The tracks on the viewer are displayed as concentric rings, from outermost to innermost: Position, Contigs/Chromosomes, CDS-forward, CDS-reverse, Non-CDS Features, GC Content, and GC Skew. Features and functionality of the viewer are described in detail below.

Circular Genome Viewer Features and Functionality

Circular Genome Viewer Main Window:

../../_images/circular_viewer_features.pngCircular Genome Viewer Features

The main window on the right side shows the circular view, which has interactive features triggered by mouseovers and mouse-clicks.

  • View the Genome information by mousing over or clicking on a contig
  • View the Feature information by mousing over or clicking on a feature

Tracks Panel:

../../_images/circular_viewer_tracks.pngCircular Genome Viewer Tracks

The Available Tracks Panel on left lists all available tracks in the Circular Viewer.

  • Show/hide tracks by clicking on the eye icon to the right of the track name.
  • Remove tracks by clicking the “X” to the right of the track name.
  • Change the color of the track or background by clicking on the small squares to the left of the track name.
  • *Add a custom track by selecting feature type, strand and keywords to show genes of interest.
  • Add a custom track of your own data by choosing the display option (Tile, Line, Histogram, or Heatmap) and choosing a file containing annotations or gene lists as GFF3 files; or RNA-Seq, ChIP-Seq, or SNP data as BigWig or BAM files.
  • Export an SVG image by clicking the Export SVG Image button.