IGB Release Documentation
Page tree

Versions Compared

Old Version 3

changes.mady.by.user David Norris

Saved on

compared with

New Version Current

changes.mady.by.user Nowlan Freese

Saved on

Key

  • This line was added.
  • This line was removed.
  • Formatting was changed.

Sprint 24 changes

Expand
titleIGBF-834 - Quitting IGB seems to be triggering the StartProtAnnot action
  • Testing Procedure

    • Select a gene model and start ProtAnnot (observe: you will see the IGB icon in Mac's dock turn into the ProtAnnot icon).

    • Close the ProtAnnot window that just opened and attempt to close IGB from the file menu.

  • Observation Checklist
    •  ProtAnnot action is not being triggered
Expand
titleIGBF-855 - Remove the "open table in new window" menu item
  • Testing Procedure
    • Start ProtAnnot from IGB
    • Open main ProtAnnot Menu
  • Observation Checklist
    •  ProtAnnot Menu no longer contains the 'open table in new window' menu item
Expand
titleIGBF-861 - Protannot NPE when selecting a gene model and sub selection of another gene model
  • Testing Procedure
    • Select the Help -> Show Console menu item
      • Leave this console open for observation during testing
    • Go to any genome
    • Select a gene model annotation and a section from an addtional gene model annotation
      • Example
      • Image Removed
    • Select the Tools Menu
    • Select Start ProtAnnot
  • Observation Checklist
    •  Verify no exceptions appear in the console and appropriate message is displayed with information on how to correct selections

 

General Function Checklist

  •  Protannot can be launched from IGB

...

    • Go to any genome
    • Select a gene model annotation
    • Select the Tools Menu
    • Select Start ProtAnnot
  •  InterProScan menu populates 
    • Select ProtAnnot menu
    • Select Load InterProScan... menu item
      • Image Removed
    • 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
      • Image Removed

...

  •   

...

 

...

General Function Checklist


  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.
  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.
  •  mac
  •  linux
  •  windows


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

Image Added

  • The ProtAnnot menu
  •  mac
  •  linux
  •  window
  • The navigation and zoom bar
  •  mac
  •  linux
  •  windows
  • The selected gene model(s) name
  •  mac
  •  linux
  •  windows
  • The Properties and InterProScan tabs
  •  mac
  •  linux
  •  windows


Image Added

  • The ProtAnnot window title contains the absolute sequence coordinates, strand direction, contig name, and the genome version.
  •  mac
  •  linux
  •  windows

 

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

Image Added

The InterProScan Job Configuration window should look as follows:

Image Added

  • Text is wrapping correctly for the information icon.
  •  mac
  •  linux
  •  windows
  • The information link directs to the appropriate "About InterPro" page.
  •  mac
  •  linux
  •  windows



  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.

Image Added

  • All job statuses are completed with a status of Finished.
  •  mac
  •  linux
  •  windows


Image Added


  • Clicking on the result cell opens the result xml on the InterProScan website.
  •  mac
  •  linux
  •  windows



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

Image Added

  • Exons have the correct protein sequences.
  •  mac
  •  linux
  •  windows



  1. In the display window, select a protein annotation to open the Properties tab.
  2. The following properties should be present and correct:

Image Added

  • Application and library name
  •  mac
  •  linux
  •  windows
  • Functional URL link
  •  mac
  •  linux
  •  windows
  • Start, end, and length coordinates
  •  mac
  •  linux
  •  windows



  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.

Image Added

  • Job statuses are Cancelled, and there are no exceptions in the Log.
  •  mac
  •  linux
  •  windows



  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.
  •  mac
  •  linux
  •  windows