ProtAnnot

General Function Checklist

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• Protannot can be launched from IGB

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• • 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

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• Checkpoint
  • sr45a should look as follows when loaded into ProtAnnot.  Take note of key items in red.

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

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• InterProScan 
  • Select ProtAnnot menu
  • Select Load InterProScan... menu item

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    • 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

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  • • • Image Added
    • Select run
      • {{ image of InterProScan results }}
      • Verify that the Exons have the correct protein sequences

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  • • • 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

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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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  • • 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.