title: Fast accessibility-based prediction of RNA-RNA interactions.
abstract: BACKGROUND
  Currently, the best RNA-RNA interaction prediction tools are based on approaches that consider both the inter- and intramolecular interactions of hybridizing RNAs. While accurate, these methods are too slow and memory-hungry to be employed in genome-wide RNA target scans. Alternative methods neglecting intramolecular structures are fast enough for genome-wide applications, but are too inaccurate to be of much practical use.
  
  
  RESULTS
  A new approach for RNA-RNA interaction was developed, with a prediction accuracy that is similar to that of algorithms that explicitly consider intramolecular structures, but running at least three orders of magnitude faster than RNAup. This is achieved by using a combination of precomputed accessibility profiles with an approximate energy model. This approach is implemented in the new version of RNAplex. The software also provides a variant using multiple sequences alignments as input, resulting in a further increase in specificity.
  
  
  BACKGROUND
  RNAplex is available at www.bioinf.uni-leipzig.de/Software/RNAplex.
authors: Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University of Leipzig, D-04107 Leipzig, Germany. htafer@bioinf.uni-leipzig.de
authors: Hakim
authors: H
authors: Tafer
authors: Fabian
authors: F
authors: Amman
authors: Florian
authors: F
authors: Eggenhofer
authors: Peter F
authors: PF
authors: Stadler
authors: Ivo L
authors: IL
authors: Hofacker