Segment-Based Scores for Pairwise and Multiple Sequence Alignments

Burkhard Morgenstern, William R. Atchley, Klaus Hahn, and Andreas Dress

In this paper, we discuss a novel scoring scheme for sequence alignments. The score of an alignment is defined as the sum of so-called weights of aligned segment pairs. A simple modification of the weight function used by the original version of the DIALIGN alignment program turns out to have a crucial advantage: it can be applied to both, global and local alignment problems without the need to specify a threshold parameter.

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