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The Query Designer is a part of UGENE genome analysis suite that allows a molecular biologist to analyze a nucleotide sequence using different algorithms (Repeats finder, ORF finder, Weight matrix matching, etc.) at the same time imposing constraints on the positional relationship of the results obtained from the algorithms.

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



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

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.

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