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Finding second and subsequent best local alignments

The Smith-Waterman algorithm returns the single best local alignment, but two proteins may share more than one common region. Waterman and Eggert [32] have shown how all local alignments may be obtained for a pair of sequences with minimal recalculation. Recently, Barton [33] has described how for a simple length dependent gap-penalty, all locally optimal alignments may be determined in the order of steps without recalculation.