Exact Pattern Matching for RNA Structure Ensembles

  • Christina Schmiedl
  • Mathias Möhl
  • Steffen Heyne
  • Mika Amit
  • Gad M. Landau
  • Sebastian Will
  • Rolf Backofen
Part of the Lecture Notes in Computer Science book series (LNCS, volume 7262)


ExpaRNA’s core algorithm computes, for two fixed RNA structures, a maximal non-overlapping set of maximal exact matchings. We introduce an algorithm ExpaRNA-P that solves the lifted problem of finding such sets of exact matchings in entire Boltzmann-distributed structure ensembles of two RNAs. Due to a novel kind of structural sparsification, the new algorithm maintains the time and space complexity of the algorithm for fixed input structures. Furthermore, we generalized the chaining algorithm of ExpaRNA in order to compute a compatible subset of ExpaRNA-P’s exact matchings. We show that ExpaRNA-P outperforms ExpaRNA in BRAliBase 2.1 benchmarks, where we pass the chained exact matchings as anchor constraints to the RNA alignment tool LocARNA. Compared to LocARNA, this novel approach shows similar accuracy but is six times faster.


Base Pair Alignment Quality Exact Pattern Multiple Structural Alignment Minimum Free Energy Structure 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • Christina Schmiedl
    • 1
  • Mathias Möhl
    • 1
  • Steffen Heyne
    • 1
  • Mika Amit
    • 2
  • Gad M. Landau
    • 2
    • 3
  • Sebastian Will
    • 1
    • 4
  • Rolf Backofen
    • 1
    • 5
  1. 1.Bioinformatics, Institute of Computer ScienceAlbert-Ludwigs-UniversitätFreiburgGermany
  2. 2.Department of Computer ScienceUniversity of HaifaHaifaIsrael
  3. 3.Department of Computer Science and EngineeringNYU-PolyBrooklynUSA
  4. 4.CSAIL and Mathematics DepartmentMITCambridgeUSA
  5. 5.Center for Biological Signaling Studies (BIOSS)Albert-Ludwigs-UniversitätFreiburgGermany

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