MicroScope - Tutorial   »   Genomic Tools   »   Circular Genome View


What is Circular Genome View ?

CGView is a Java package which allows to produce high quality, zoomable maps of circular genomes. Its primary purpose is to serve as a component of sequence annotation pipelines, as a mean of generating visual output suitable for the web. Starting with information of one genome and the features to visualize, CGView converts the input into a graphical map (PNG, JPG, or Scalable Vector Graphics format) and completes it with labels, a title, legends, and footnotes.

More: http://wishart.biology.ualberta.ca/cgview/index.html

Reference: Stothard P, Wishart DS. Circular genome visualization and exploration using CGView. Bioinformatics. 2005 Feb 15;21(4):537-9

How to use the Circular Genome View ?

When you select the Circular Genome View functionality you obtain a global circular map of the selected sequence. Circles display (from the outside):

  • (1) GC percent deviation (GC window - mean GC) in a 1000-bp window.
  • (2) Predicted CDSs transcribed in the clockwise direction.
  • (3) Predicted CDSs transcribed in the counterclockwise direction.
  • (4) GC skew (G+C/G-C) in a 1000-bp window.
  • (5) rRNA (blue), tRNA (green), misc_RNA (orange), Transposable elements (pink) and pseudogenes (grey).

Genes displayed in (2) and (3) are color-coded according different categories:

  • red and blue, MaGe validated annotations ;
  • orange: MicroScope automatic annotation with a reference genome ;
  • purple: Primary / Automatic annotations.

In addition to the default full view map, the program can generate a series of hyperlinked maps showing expanded views. You can use the CG View toolbar to navigate into the circular map.

(PNG)

Only the 5 first buttons are active on the toolbar:

  • Zoom out
  • Zoom in
  • View entire map
  • Move counterclockwise
  • Move clockwise

If you click on a gene name/label it open the corresponding Gene window giving you access the full annotation of the gene.