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In UGENE you can create a data processing workflows with a help of the Workflow Designer. To use the Workflow Designer go to the Tools-->Workflow Designer:

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The following window appears:

Workflow Designer. UGENE Workflow Designer is a part of UGENE genome analysis suite that allows a molecular biologist to create and run complex computational workflows even if he or she is not familiar with any programming language. The workflows comprise reproducible, reusable and self-documented research routines, with a simple and unambiguous visual representation suitable for publications. The workflows can be run both locally and remotely, either using graphical interface or launched from the command line. The elements that a workflow consists of corresponds to the bulk of algorithms integrated into UGENE. Additionally you can create custom workflow elements.

To launch the Workflow Designer select the Tools ‣ Workflow Designer item in the UGENE main menu. The following window appears: 

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Example 4: You can find ORFs pattern in a sequence and save it as annotations using the following workflow: 

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Create the workflow, choose parameters and click the Run button. The output file is your sequence with the pattern as annotation.

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