title: Fast prediction of RNA-RNA interaction.
abstract: BACKGROUND
  Regulatory antisense RNAs are a class of ncRNAs that regulate gene expression by prohibiting the translation of an mRNA by establishing stable interactions with a target sequence. There is great demand for efficient computational methods to predict the specific interaction between an ncRNA and its target mRNA(s). There are a number of algorithms in the literature which can predict a variety of such interactions--unfortunately at a very high computational cost. Although some existing target prediction approaches are much faster, they are specialized for interactions with a single binding site.
  
  
  METHODS
  In this paper we present a novel algorithm to accurately predict the minimum free energy structure of RNA-RNA interaction under the most general type of interactions studied in the literature. Moreover, we introduce a fast heuristic method to predict the specific (multiple) binding sites of two interacting RNAs.
  
  
  RESULTS
  We verify the performance of our algorithms for joint structure and binding site prediction on a set of known interacting RNA pairs. Experimental results show our algorithms are highly accurate and outperform all competitive approaches.
authors.affiliation: School of Computing Science, Simon Fraser University, Burnaby, Canada.
authors.forename: Raheleh
authors.initials: R
authors.lastname: Salari
authors.forename: Rolf
authors.initials: R
authors.lastname: Backofen
authors.forename: S Cenk
authors.initials: SC
authors.lastname: Sahinalp