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International Symposium on String Processing and Information Retrieval

SPIRE 2015: String Processing and Information Retrieval pp 116-123 | Cite as

Chaining Fragments in Sequences: to Sweep or Not (Extended Abstract)

  • Julien AllaliEmail author
  • Cedric Chauve
  • Laetitia Bourgeade
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 9309)

Abstract

Computing an optimal chain of fragments is a classical problem in string algorithms, with important applications in computational biology. There exist two efficient dynamic programming algorithms solving this problem, based on different principles. In the present note, we show how it is possible to combine the principles of two of these algorithms in order to design a hybrid dynamic programming algorithm that combines the advantages of both algorithms.

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Copyright information

© Springer International Publishing Switzerland 2015

Authors and Affiliations

  • Julien Allali
    • 1
    • 2
    Email author
  • Cedric Chauve
    • 2
    • 3
  • Laetitia Bourgeade
    • 1
  1. 1.LaBRIUniversité BordeauxTalenceFrance
  2. 2.ENSEIRB-MATMECABordeaux INPTalenceFrance
  3. 3.Department of MathematicsSimon Fraser UniversityBurnabyCanada

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