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Line geometries for sequence comparisons

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Abstract

Well-known dynamic programming algorithms exist for comparing two finite sequences inO(N 2) time and storage, whereN is the common sequence length. Extensions to the comparison ofM finite sequences requireO((2N) M) time and storage, making such algorithms difficult even forM=3. A simple generalization of the sequences makes it possible to obtain some results about the geometry of sequence alignments. These ideas suggest heuristic approaches to problems of comparing several sequences. IfM sequences are known to be related by a binary tree, they can be aligned inO(MN 2) time andO(N 2+NM) storage.

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Authors and Affiliations

  1. Department of Mathematics and of Molecular Biology, 90089-1113, Los Angeles, CA, U.S.A.

    Michael S. Waterman & Marcela D. Perlwitz

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  1. Michael S. Waterman
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  2. Marcela D. Perlwitz
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This work was supported by a grant from the System Development Foundation.

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Waterman, M.S., Perlwitz, M.D. Line geometries for sequence comparisons. Bltn Mathcal Biology 46, 567–577 (1984). https://doi.org/10.1007/BF02459504

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