Journal
BIOINFORMATICS
Volume 27, Issue 14, Pages 1934-1940Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/btr281
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Funding
- European Union
- DFG [SPP1258]
- Austrian GENAU project 'Regulatory Noncoding RNA'
- Austrian Science Fund (FWF) [W1207] Funding Source: Austrian Science Fund (FWF)
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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.
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