GenDBWiki/WebDocumentation/DialogWindows/OrthologViewer

Ortholog Viewer

The Ortholog Viewer is a tool that shows ortholog CDS in similar genomes. The orthologs have to be computed before.

What should be done to use this tool? (Points 1-3 are already done, if you prepared the project for the Comparative Annotator

1. create Bidirectional-Blast-Tools in the project with: create_genome_compare_tools.pl
   
2. Run the Tool for each Contig-combination with: submit_job.pl
   
3. Run set_biderectional_project_config.pl.
   
4. Run compute_orthologs.pl to create ortholog-observations
   
5. Use the tool
   

This is how the window looks like after opening the Ortholog Viewer:

Now you can do the following:

• Browse through the genome
• Select a CDS

Anchor(Browse Orthologs)

Browse through the genome

You can browse through the genome, using the scrollbar. When moving the mouse over a CDS-box, its orthologs are highlighted yellow:
File:GenDBWiki$$WebDocumentation$$DialogWindows$$OrthologViewer$ortholog viewer 2.gif

When you find an interesting CDS you may examine it further by selecting it.

Select a CDS

By clicking a CDS-box, one CDS is selected (red) and its orthologs are marked orange. Information about all highlighted CDS are shown below the image. Loading the information may take some seconds. Please be patient.

After selecting a CDS you get a menu:

You can open the Comparative Annotator or select the chosen CDS in the Main-Window.