ProtAnnot

General Function Checklist

• ProtAnnot is be launched from IGB

• • Install the ProtAnnot plugin through the App Manager (Tools>Open App Manager)
  • Select any genome
  • Select one or more whole gene model annotation
  • Select the Tools Menu
  • Select Start ProtAnnot

• Checkpoint
  • Your selected gene model(s) should look as follows when loaded into ProtAnnot; take note of the following key items in red:
    • The window title
    • The ProtAnnot menu
    • The navigation and zoom bar
    • Th selected gene model(s) name
    • The Properties and InterProScan tabs
      

• • The ProtAnnot window title should contain the absolute sequence coordinates, strand direction, contig name, and the genome version. 

• InterProScan 
  • Select ProtAnnot menu
  • Select Load InterProScan... menu item
    • 
      
  • Verify the InterProScan Job Configuration window appears similar to the image below
    • Verify tool tips in the information icon wrap appropriately
    • Verify the link in the highlighted box below links to the appropriate InterProScan about page
    • 
  • Select run
    • {{ image of InterProScan results }}
    • Verify that the Exons have the correct protein sequences

• • • Select an InterProScan result and verify that the properties are correct
      • Correct start, end, and length.
      • Functioning URL when clicked
      • Application and library name are present

• • Open the InterProScan tab
    • Verify that that both jobs have a status of FINISHED
    • Clicking on the result cell should open the result xml on the InterProScan website

• • Run InterProScan again by selection "Run InterProScan" under the InterProScan tab.  See image above.
  • Once the jobs are running select "Cancel All Jobs" under the InterProScan tab
  • Verify that the job statuses are "Cancelled" and that there are no exceptions in the logs.

o   Your selected gene model(s) should look as follows when loaded into ProtAnnot. Take note of the following key items in red:

§   The Window Title

§  The ProtAnnot Menu

§  The navigation and zoom bar

§  The selected gene model(s) name

§  The Properties and InterProScan tabs