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)

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• Please note, to simulate the images in this testing module, select gene model annotations that are adjacent to one another, rather than annotations that are far apart. Selecting annotations that are far apart will cause ProtAnnot to display a view that is significantly more zoomed out compared to the images in this testing module. However, this can be adjusted with the zoom bar feature. 

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1. 1. It may be helpful to watch this How to use ProtAnnot YouTube video if you are unfamiliar with using ProtAnnot.
2. Open the A_thaliana_Jun_2009 genome.
3. Navigate to the following gene: Chr1:2,257,247-2,260,234
4. 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.
5. Select the Tools Menu.
6. Select Start ProtAnnot.

• 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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1. Select the ProtAnnot

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

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The InterProScan Job Configuration window

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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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should 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 may not return jobs. 
2. Click Run.
3. Select the InterProScan 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
should open
• opens the result xml on the InterProScan website

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1. Select the Properties tab

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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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• 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.
2. 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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