ProtAnnot

General Function Checklist

• Protannot can be launched from IGB

·          

• • Install the ProtAnnot plugin through the App Manager (Tools > Open App Manager)
  • Go to any genome
  • Select one or more whole gene model annotation
  • Select the Tools Menu
  • Select Start ProtAnnot from the Tools Menu
• Checkpoint
  • sr45a should look as follows when loaded into ProtAnnot.  Take note of key items in red.

·          

• • 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

·          
o     

• • • 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.