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:
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If you want to save the results as annotations input the annotations saving parameters (Annotation name, Group name, a file to save the annotation to). Also you can add qualifier with corresponding pattern subsequences to result annotations. Check the corresponding checkbox for it.
If you want to save the results as multiple alignment select the following parameters:
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