Alignment with Non-overlapping Inversions on Two Strings

  • Da-Jung Cho
  • Yo-Sub Han
  • Hwee Kim
Part of the Lecture Notes in Computer Science book series (LNCS, volume 8344)


The inversion is one of the important operations in bio sequence analysis and the sequence alignment problem is well-studied for efficient bio sequence comparisons. Based on inversion operations, we introduce the alignment with non-overlapping inversion problem: Given two strings x and y, does there exist an alignment with non-overlapping inversions for x and y. We, in particular, consider the alignment problem when non-overlapping inversions are allowed for both x and y. We design an efficient algorithm that determines the existence of non-overlapping inversions and present another efficient algorithm that retrieves such an alignment, if exists.


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Copyright information

© Springer International Publishing Switzerland 2014

Authors and Affiliations

  • Da-Jung Cho
    • 1
  • Yo-Sub Han
    • 1
  • Hwee Kim
    • 1
  1. 1.Department of Computer ScienceYonsei UniversitySeoulRepublic of Korea

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