COCOON 2007: Computing and Combinatorics pp 151-164

Alignments with Non-overlapping Moves, Inversions and Tandem Duplications in O(n4) Time

  • Christian Ledergerber
  • Christophe Dessimoz
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4598)

Abstract

Sequence alignment is a central problem in bioinformatics. The classical dynamic programming algorithm aligns two sequences by optimizing over possible insertions, deletions and substitution. However, other evolutionary events can be observed, such as inversions, tandem duplications or moves (transpositions). It has been established that the extension of the problem to move operations is NP-complete. Previous work has shown that an extension restricted to non-overlapping inversions can be solved in O(n3) with a restricted scoring scheme. In this paper, we show that the alignment problem extended to non-overlapping moves can be solved in O(n5) for general scoring schemes, O(n4logn) for concave scoring schemes and O(n4) for restricted scoring schemes. Furthermore, we show that the alignment problem extended to non-overlapping moves, inversions and tandem duplications can be solved with the same time complexities. Finally, an example of an alignment with non-overlapping moves is provided.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2007

Authors and Affiliations

  • Christian Ledergerber
    • 1
  • Christophe Dessimoz
    • 1
  1. 1.ETH Zurich, Institute of Computational ScienceSwitzerland

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