About the Query Designer

The Query Designer allows a molecular biologist to analyze a nucleotide sequence using different algorithms (Repeats finder, ORF finder, Weight matrix matching, etc.) while imposing constraints on the positional relationship of the results obtained from these algorithms.

A user-friendly interface is used to create a schema of the algorithms and constraints.

Alternatively, you can create or edit a schema using a text editor.

Once the schema has been created and all its parameters set, you can run it on a nucleotide sequence. The results are saved as a set of annotations in the specified file in the Genbank format. Additionally, when you have a query designer schema, you can analyze a nucleotide sequence from the sequence view using this schema by selecting the Analyze->Analyze with query schema context menu item.