Smith-Waterman plugin

Smith-Waterman plugin adds a complete implementation of Smith-Waterman algorithm to UGENE.

Usage example:

Open a DNA or protein sequence in Sequence view and use "Analyse->Find pattern [Smith-Waterman]" item in popup menu:

In fact, Smith-Waterman algorithm is the most optimized algorithm in UGENE. As you can see from the picture, UGENE contains SSE2 and CUDA optimizations for the algorithm (but only on the systems which have SSE-capable CPU and CUDA-enabled GPU).

A quick guide on dialog parameters:

• Version — implementation of the algorithm. Non-classic versions produce the same results as classic but much faster.
• Scoring matrix — can be chosen from bunch of matrices supplied with UGENE (and viewed with the corresponding button).
• Filtering strategy — a simple heuristic which told UGENE to filter intersected hits. If set to none, algorithm will report large sets 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.
• Other parameters, as we hope, are self-descriptive.

The regions found are saved as annotations to the sequence: