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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. 

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•  InterProScan 
  • Select the ProtAnnot menu
  • Select Load Run InterProScan... menu item
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  •  Verify that the InterProScan Job Configuration window appears similar to the image below
    • Verify
  tool tips in
  • • correct text wrapping for the information icon
  wrap appropriately
  • • 
      
    • Verify that the
  link in the highlighted box below links
  • • information link directs to the appropriate
  InterProScan about
  • • "About InterPro" page
      
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•  Select run
• {{ image of InterProScan results }}
Verify that the Exons Run
• Select the InterProScan tab
  •  Verify that all job statuses are completed with a status of FINISHED.

...

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

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• • 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.

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• Run InterProScan again by selection "Run InterProScan" under the InterProScan tab.  See image above.
  • •  In the display window, select a protein annotation to open the Properties tab, and verify that the following properties are
    correct
  • Correct start, end, and length.
  • Functioning URL when clicked
  • present and correct:
    
    • Application and library name
  are present

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• • 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

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• • • • Functional URL link
      • Start, end, and length coordinates

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• •  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
  the
  • • job statuses are
  "Cancelled"
  • • CANCELLED, and that there are no exceptions in the logs
  .

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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

o   Verify that the InterProScan Job Configuration window appears similar to the image below, as well as the following items:

§   Verify correct text wrapping for the information icon

§  Verify that the information link directs to the appropriate "About InterPro" page