Exact pattern matching for RNA structure ensembles

Authors:
Christina Schmiedl;Mathias Möhl;Steffen Heyne;Mika Amit;Gad M. Landau;Sebastian Will;Rolf Backofen
Affiliations:
Bioinformatics, Institute of Computer Science, Albert-Ludwigs-Universität, Freiburg, Germany;Bioinformatics, Institute of Computer Science, Albert-Ludwigs-Universität, Freiburg, Germany;Bioinformatics, Institute of Computer Science, Albert-Ludwigs-Universität, Freiburg, Germany;Department of Computer Science, University of Haifa, Haifa, Israel;Department of Computer Science, University of Haifa, Haifa, Israel and Department of Computer Science and Engineering, NYU-Poly, Brooklyn, NY;Bioinformatics, Institute of Computer Science, Albert-Ludwigs-Universität, Freiburg, Germany and CSAIL and Mathematics Department, MIT, Cambridge, MA;Bioinformatics, Institute of Computer Science, Albert-Ludwigs-Universität, Freiburg, Germany and Center for Biological Signaling Studies (BIOSS), Albert-Ludwigs-Universität, Freiburg, Ge ...
Venue:
RECOMB'12 Proceedings of the 16th Annual international conference on Research in Computational Molecular Biology
Year:
2012

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Abstract

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.