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The Smith-Waterman Search plugin adds a complete implementation of the Smiththe Smith-Waterman algorithm to algorithm to UGENE.

To use the plugin open a nucleotide or protein sequence in the Sequence View and select the Analyze ‣ Find pattern [Smith-Waterman] item in the context menu. The Smith-Waterman Search dialog appears:


If you want to save the results as annotations input the annotations saving parameters (Annotation nameGroup name, a file to save the annotation to).