Prepare a query schema and save it to a file.

Open a nucleotide sequence that you want to analyze with this query schema. You can see the sequence displayed in the Sequence view.

Select the Analyze ‣ Analyze with Query Schema item in the Actions main menu or in the context menu:

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     <img src="/wiki/download/attachments/16122046/Running Schema from the Sequence View.png"/>
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The Analyze with query schema dialog appears:

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     <img src="/wiki/download/attachments/16122046/Running Schema from the Sequence View_1.png"/>
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Browse for the file with a query schema. The selected schema preview appears in the dialog, for example:

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     <img src="/wiki/download/attachments/16122046/Running Schema from the Sequence View_2.png"/>
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You can also adjust other parameters:

Region — the sequence range to analyze with the query schema, you can select:

• • Whole sequence — to analyze the whole sequence.
  • Selected range — to analyze the currently selected sequence region. This item is disabled if there is no region selected.
  • Custom range — to specify manually a range to analyze.

In the Save annotation(s) to group you can set up a file to store annotations.  It could be either an existing annotation table object, a new annotation table or auto-annotations table (if it is available).

In the Annotation parameters group you can specify the name of the group. If the group name is set to <auto> UGENE will use the group name as the name for the group. Also you can add a description in the corresponding text field.