Fast accessibility-based prediction of RNA-RNA interactions

Bioinformatics. 2011 Jul 15;27(14):1934-40. doi: 10.1093/bioinformatics/btr281. Epub 2011 May 18.


Motivation: 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.

Availability: RNAplex is available at

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Base Sequence
  • Genome
  • Models, Molecular*
  • RNA / chemistry*
  • RNA / genetics
  • Sequence Analysis, RNA / instrumentation
  • Sequence Analysis, RNA / methods*
  • Software*


  • RNA