Local exact pattern matching for non-fixed RNA structures

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

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


Detecting local common sequence-structure regions of RNAs is a biologically meaningful problem. By detecting such regions, biologists are able to identify functional similarity between the inspected molecules. We developed dynamic programming algorithms for finding common structure-sequence patterns between two RNAs. The RNAs are given by their sequence and a set of potential base pairs with associated probabilities. In contrast to prior work which matches fixed structures, we support the arc breaking edit operation; this allows to match only a subset of the given base pairs. We present an O(n 3) algorithm for local exact pattern matching between two nested RNAs, and an O(n 3logn) algorithm for one nested RNA and one bounded-unlimited RNA.

Original languageEnglish
Title of host publicationCombinatorial Pattern Matching - 23rd Annual Symposium, CPM 2012, Proceedings
Number of pages15
StatePublished - 2012
Event23rd Annual Symposium on Combinatorial Pattern Matching, CPM 2012 - Helsinki, Finland
Duration: 3 Jul 20125 Jul 2012

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume7354 LNCS
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349


Conference23rd Annual Symposium on Combinatorial Pattern Matching, CPM 2012

ASJC Scopus subject areas

  • Theoretical Computer Science
  • General Computer Science


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