Abstract
Recently algorithms for parametric alignment (Watermanet al., 1992,Natl Acad. Sci. USA 89, 6090–6093; Gusfieldet al., 1992,Proceedings of the Third Annual ACM-SIAM Discrete Algorithms) find optimal scores for all penalty parameters, both for global and local sequence alignment. This paper reviews those techniques. Then in the main part of this paper dynamic programming methods are used to compute ensemble alignment, finding all alignment scores for all parameters. Both global and local ensemble alignments are studied, and parametric alignment is used to compute near optimal ensemble alignments.
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Waterman, M.S. Parametric and ensemble sequence alignment algorithms. Bltn Mathcal Biology 56, 743–767 (1994). https://doi.org/10.1007/BF02460719
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DOI: https://doi.org/10.1007/BF02460719