Smith-Waterman Search¶

The Smith-Waterman Search plugin adds a complete implementation of the Smith-Waterman 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:

First of all you need to specify the pattern to search for. The rest parameters are optional:

Search in — select either to search in the sequence or in its translation.

Strand — select the strand to search in: direct, complementary or both strands.

Range — specifies the region of the sequence that will be used to search for the pattern. By default, if a subsequence has been selected when the dialog has been opened, then the selected subsequence is searched for the pattern. Otherwise, the whole sequence is used. You can also input a custom range.

Algorithm version — version of the algorithm implementation. Non-classic versions produce the same results as classic but much faster. To use these optimizations your system must support these capabilities.

• Classic 2
• SSE2
• CUDA
• OPENCL

Scoring matrix — can be chosen from a bunch of matrices supplied with UGENE. To view a matrix selected click the View button.

Gap open — penalty for opening a gap.

Gap extension — penalty for extending a gap

Report results — simple heuristic which allows to filter intersected hits. If it is set to none, the algorithm may report large set of almost identical results in the same region.

Minimal score — another simple heuristic which measures sequences similarity. It is more convenient than using some abstract scores. If set to 100%, the algorithm will search for exact substring match.

The results of the search are saved as annotations. To set the annotations parameters (Annotation name, Group name, a file to save the annotation to) go to the Input and output tab of the dialog.