How to Create and Run Schema

• Select the Tools ‣ Query Designer item in the main menu.

Result: The Query Designer window appears:

• Drag the Repeats element from the Palette to the Scene.

Result: The Repeats element subunits are presented on the Scene:

Note that by default, the minimum distance between left and right repeats is 0 bp, and the maximum distance is 5000 bp.

• Slide the Repeats element subunits apart.

Result:

• Drag the ORF element from the Palette and drop it between the repeats.

Result: The ORF element is presented on the Scene:

• Find the End-Start constraint on the Palette:

And drag it between the left Repeats element and ORF.

Result: The dialog appears:

• Check that From equals Repeats.left and To equals ORF. Set Max to 5000. Press the OK button.

Result: The constraint has been added to the elements:

• Repeat steps 5-6 for the ORF element and the right Repeats subunit.

Result: The schema looks as follows:

• Press the Run Schema button on the toolbar:

Result: The Run schema dialog appears:

• Browse for the sequence to analyze (the Load sequence field) and for a GenBank file to save results to (the Save results to field). Click the Run button.

Result: Both the sequence and the file with annotations are added to the current project. The sequence appears in the Sequence View window, for example:

To learn more about the Sequence View, read the main UGENE User Manual.

The schema described in this example is also available as a sample schema. Select the Samples tab on the Palette and double-click ORF-Repeats to open the sample schema.