General Function Checklist

ProtAnnot is launched from IGB

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1. Install the ProtAnnot plugin through the IGB App Manager (Tools > Open App Manager)
   1. It may be helpful to watch this How to use ProtAnnot YouTube video if you are unfamiliar with using ProtAnnot.

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1. Open the A_thaliana_Jun_2009 genome.
2. Navigate to the following gene: Chr1:2,257,247-2,260,234
3. Select the AT1G07350.1 and AT1G07350.2 gene models by shift-clicking both models. Make sure that the full model is selected, and not an individual exon.
4. Select the Tools Menu.
5. Select Start ProtAnnot

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1. .

• ProtAnnot is launched from IGB.

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

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• The ProtAnnot menu

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• The navigation and zoom bar

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• The selected gene model(s) name

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• The Properties and InterProScan tabs

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

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InterProScan 

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1. Select the ProtAnnot

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1. menu.
2. Select Run InterProScan menu item.

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Verify that the The InterProScan Job Configuration window appears similar to the image belowshould look as follows:

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• Text is wrapping correctly for the information icon.
  

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• The information link directs to the appropriate "About InterPro" page.
  

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1. Provide an email address in the Email field.
   1. An email address is required for running InterProScan. Otherwise, InterProScan

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1. 1. may not return

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• For testing purposes, please note that if an invalid email address is provided, the user may not see any jobs running.

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1. 1. jobs. 
2. Click Run.
3. Select the InterProScan

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1. tab.

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• All job statuses are completed with a status of

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• Finished.

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• Clicking on the result cell

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• opens the result xml on the InterProScan website.

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1. Select the Properties tab.
2. In the display window, select a gene model to open the Properties tab

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• Exons have the correct protein sequences.

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1. In the display window, select a protein annotation to open the Properties tab

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2. The following properties

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1. should be present and correct:

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• Application and library name

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Application and library name
• Functional URL link

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• Start, end, and length coordinates

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1. Run the InterProScan again by selecting Run InterProScan under the InterProScan tab.

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1. Once the jobs are running, select Cancel All Jobs under the InterProScan tab

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• Job statuses are
CANCELLED
• Cancelled, and
that
• there are no exceptions in
the logs

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• the Log.

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1. Select ProtAnnot in the top left of the ProtAnnot window, and then choose Save Image...
2. Save the image to your machine, then open the file.

• The image is viewable and saved appropriately.

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