MicroScope - Tutorial   »   Variant Discovery   »   Evolution Projects   »   Graphical Analysis


What is the aim of the Graphical Analysis tool ?

To visualize the distribution of a specific clone’s mutations along the circular representation of a reference genome.

And to detect potential hot spots of mutations.

How to use this tool ?

This tool is based on the Java applet CGView.

(PNG)
  1. Choose a reference sequence.
  2. Select the clone for which you want to visualize the mutations.
  3. If you want, you can specify:
    • the nature of the relevant mutations,
    • their location on the reference genome,
    • the sequencing technology used to produce the data from which the mutations have been predicted,
    • the mutation score,
    • the portion of the reference sequence which must be screened, and
    • the length of the mutations.
  4. Launch the CGView applet.

Trick: You can decide which Genomic Objects (GOs) and corresponding labels will be displayed on the circular map thanks to the two selection lists situated next to the CGView button.

What can you see on the graphical representation ?

Circles display (from the outside):
(1) Predicted mutational events (SNPs, insertions, deletions ).
(2) Predicted CDSs transcribed in the clockwise direction (Primary/Automatic annotations, MicroScope automatic annotation with a reference genome, MaGe validated annotations).
(3) Predicted CDSs transcribed in the counterclockwise direction (Primary/Automatic annotations, MicroScope automatic annotation with a reference genome, MaGe validated annotations).
(4) Transposable elements and pseudogenes.

Tip1: Each GO label encompasses a link to the information form of the Genomic Object considered.
Tip2: If you mouseover a mutation label, a more complete description will appear at the bottom of the CGView applet.
Tip3: The image obtained can be downloaded in the .svgz format (hyperlink just under the applet)