ProtAnnot

General Function Checklist

• ProtAnnot is 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 the ProtAnnot menu
  • Select Run InterProScan menu item
    • 
      
  • Verify that the InterProScan Job Configuration window appears similar to the image below
    • Provide a valid email address; this is required for running InterProScan. Otherwise, InterProScan does not return any jobs.
      • For testing purposes, please note that if an invalid email address is provided, the user may night see any jobs running.
    • Verify correct text wrapping for the information icon
      
    • Verify that the information link directs to the appropriate "About InterPro" page
      

• Select Run
  • Select the InterProScan tab
    • Verify that all job statuses are completed with a status of FINISHED.

• • • Clicking on the result cell should open the result xml on the InterProScan website

• • Select the Properties tab
    • In the display window, select a gene model to open the Properties tab, and verify that exons have the correct protein sequences.

• • • In the display window, select a protein annotation to open the Properties tab, and verify that the following properties are present and correct:
      
      • Application and library name
      • Functional URL link
      • Start, end, and length coordinates

• • Run the InterProScan again by selecting Run InterProScan under the InterProScan tab
    • Once the jobs are running, select Cancel All Jobs under the InterProScan tab
    • Verify that job statuses are CANCELLED, and that there are no exceptions in the logs