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Searching with dynamic programming

Dynamic programming requires a matrix of pair scores and a gap penalty and will return the best score for aligning the two sequences (See section 3.2). Both local and global alignment methods may be applied to database scanning, but local alignment methods are more useful since they do not make the assumption that the query protein and database sequence are of similar length.

Although it is feasible to use dynamic programming to search databases on a desktop computer (Section 6.2) the technique has not generally been adopted for database searching. This is mainly because fast implementations of the Smith-Waterman and similar algorithms (e.g. see [33]) have not been widely available until recently.