Fast RNA structure alignment for crossing input structures

Rolf Backofen, Gad M. Landau, Mathias Möhl, Dekel Tsur, Oren Weimann

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


The complexity of pairwise RNA structure alignment depends on the structural restrictions assumed for both the input structures and the computed consensus structure. For arbitrarily crossing input and consensus structures, the problem is NP-hard. For non-crossing consensus structures, Jiang et al's algorithm [1] computes the alignment in O(n 2 m 2) time where n and m denote the lengths of the two input sequences. If also the input structures are non-crossing, the problem corresponds to tree editing which can be solved in O(m2n(1 + log n/m))time [2]. We present a new algorithm that solves the problem for d-crossing structures in O(d m 2 nlogn) time, where d is a parameter that is one for non-crossing structures, bounded by n for crossing structures, and much smaller than n on most practical examples. Crossing input structures allow for applications where the input is not a fixed structure but is given as base-pair probability matrices.

Original languageEnglish
Title of host publicationCombinatorial Pattern Matching - 20th Annual Symposium, CPM 2009, Proceedings
Number of pages13
StatePublished - 2009
Event20th Annual Symposium on Combinatorial Pattern Matching, CPM 2009 - Lille, France
Duration: 22 Jun 200924 Jun 2009

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume5577 LNCS
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349


Conference20th Annual Symposium on Combinatorial Pattern Matching, CPM 2009


  • RNA
  • Sequence structure alignment
  • Simultaneous alignment and folding

ASJC Scopus subject areas

  • Theoretical Computer Science
  • General Computer Science


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