...
When the schema has been created and all its parameters have been set you can run it for a nucleotide sequence. The results are saved as a set of annotations to the specified file in the Genbank format. Also when you have query designer scheme you can analyze a nucleotide sequence from the sequence view with a help of this schema. Call the Analyze->Analyze with query schema context menu item for this.
To learn more about the Query Designer read the Query Designer Manual (follow the link on the UGENE documentation page)