MacVector: Aligning Sequences

MacVector™ uses a variation (1 ) of the Wilbur-Lipman-Pearson algorithm (2 –5 ) to find a “best” pairwise alignment between a single query sequence in memory and one or more other sequences stored in a folder on disk. The algorithm uses three comparison steps. A very rapid technique called hashing is used to find regions of the two sequences that contain N consecutive matches. The region surrounding each matching nucleus is then scored, using match and mismatch values defined by the user. If this initial score for a matching region exceeds a cutoff score, an optimal alignment is performed, inserting deletions and gaps as necessary to improve the score. The alignment with the best optimized score is saved and reported to the user.