A Propagator for Maximum Weight String Alignment with Arbitrary Pairwise Dependencies

  • Alessandro Dal Palù
  • Mathias Möhl
  • Sebastian Will
Part of the Lecture Notes in Computer Science book series (LNCS, volume 6308)

Abstract

The optimization of weighted string alignments is a well studied problem recurring in a number of application domains and can be solved efficiently. The problem becomes MAX-SNP-hard as soon as arbitrary pairwise dependencies among the alignment edges are introduced. We present a global propagator for this problem which is based on efficiently solving a relaxation of it. In the context of bioinformatics, the problem is known as alignment of arc-annotated sequences, which is e.g. used for comparing RNA molecules. For a restricted version of this alignment problem, we show that a constraint program based on our propagator is on par with state of the art methods. For the general problem with unrestricted dependencies, our tool constitutes the first available method with promising applications in this field.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2010

Authors and Affiliations

  • Alessandro Dal Palù
    • 1
  • Mathias Möhl
    • 2
  • Sebastian Will
    • 2
    • 3
  1. 1.Dipartimento di MatematicaUniversità degli Studi di ParmaParmaItaly
  2. 2.Bioinformatics, Institute of Computer ScienceAlbert-Ludwigs-UniversitätFreiburgGermany
  3. 3.Computation and Biology LabCSAIL, MITCambridgeUSA

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