Segment-Based Scores for Pairwise and Multiple Sequence Alignments

@article{Morgenstern1998SegmentBasedSF,
  title={Segment-Based Scores for Pairwise and Multiple Sequence Alignments},
  author={Burkhard Morgenstern and William R. Atchley and Klaus Hahn and Andreas W. M. Dress},
  journal={Proceedings. International Conference on Intelligent Systems for Molecular Biology},
  year={1998},
  volume={6},
  pages={115-21}
}
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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