Segment-Based Scores for Pairwise and Multiple Sequence Alignments

Proceedings Of The Sixth International Conference On Intelligent Systems For Molecular Biology

Volume

Proceedings Of The Sixth International Conference On Intelligent Systems For Molecular Biology

Contents

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.