Exact pattern matching for RNA structure ensembles

Christina Schmiedl, Mathias Möhl, Steffen Heyne, Mika Amit, Gad M. Landau, Sebastian Will, Rolf Backofen

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review


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.

Original languageEnglish
Title of host publicationResearch in Computational Molecular Biology - 16th Annual International Conference, RECOMB 2012, Proceedings
Number of pages16
StatePublished - 2012
Event16th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2012 - Barcelona, Spain
Duration: 21 Apr 201224 Apr 2012

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume7262 LNBI
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349


Conference16th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2012

ASJC Scopus subject areas

  • Theoretical Computer Science
  • General Computer Science


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