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Complete the following  general function checklist to verify that the Search subsystem is operating as expected.

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General Function Checklist


  1. Open the H_sapiens_Dec_2013 genome.
  2. Type dmd in the Quick-search box.Verify that "

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  • DMD

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  • is one of the suggested matches in the Quick-search drop-down.
  •  Mac
  •  Linux
  •  Windows

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Select

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DMD

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 from the Quick-search drop-down to navigate to the longest known gene in the human genome, the dystrophin gene (DMD).

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  • IGB has navigated to the proper gene (dystrophin). You can do this by viewing the selection info for the gene. The gene's title should be "DMD". 
    *(Known issue. See IGBF-2625).
  •  Mac
  •  Linux
  •  Windows

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Select the Advanced Search tab at the bottom of IGB.

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  • Search results for

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  • DMD

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  •  are already being displayed in the tab.
  •  Mac
  •  Linux
  •  Windows

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Select the top search result in the Advanced Search tab (ID:

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NM_001166237

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, Title:

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GSDMD

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).

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  • IGB has navigated to

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  • NM_001166237

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  •  in the gene

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  • GSDMD

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  • .
  •  Mac
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  •  Windows

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Navigate to the following coordinates: chr1:30,688,740-31,361,080

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  • IGB has navigated to the proper location.
  •  Mac
  •  Linux
  •  Windows

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  1. In the Advanced Search tab at the bottom IGB, select Residues from the search type drop-down menu.
  2. Enter "TAG|TAA|TGA" into the Advanced Search textbox and start the search.

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  • Verify that the search has located matches for "TAG", "TAA", and "TGA".
  •  Mac
  •  Linux
  •  Windows

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Navigate to the following coordinates: chr1:30,992,236-30,992,279

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  • Residues have been highlighted on the sequence axis.
  •  Mac
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  •  Windows

  1. Image RemovedEnter "Navigate to the following coordinates: chr1:30,688,740-31,361,080" into the Quick search box to navigate to the specified coordinates. 
  2. In the Advanced search PanelSearch tab at the bottom of IGB, select Residues from the search type drop-down menu.
  3. Enter the following regular expressions .(Note - clear the search results between each search (click the red X).):
      "
      1. TATATttatg
      "
      "
      1. TATA.ttatg
      "
      "
      1. TATA..tatg
      "
      "
      1. TAT[AT]Tttatg
      "
      "
      1. [TA]{1,3}Tttatg
      "
      "
      1. TATAt*atg
      "
      "
      1. TATAT.*ttatg
      "
      "
      1. TATAT.*?ttatg
      "Verify that there are results
    • Results show up for each search conducted above.
    •  Mac
    •  Linux
    •  Windows


    1. In the Advanced Search tab, select Properties from the search type drop-down menu.
    2. Enter "false" in the search text box.  Verify that there
    • There are many results and if you select one (double-click it) and go to the Selection Info panel, there is at least one attribute that has the value

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    • false

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    • .
    •  Mac
    •  Linux
    •  Windows

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    Enter family

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    in the search text box.

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    • There are many results and all include the

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    • word family

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    • in the description.

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    • If not, check the selection info panel

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    • .
    •  Mac
    •  Linux
    •  Windows

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