RIsearch

RIsearch is a software tool designed to predict putative RNA-RNA duplexes in a genome-wide scale. It uses a simplified Turner energy model to pre-filter the duplexes, significantly reducing runtime while maintaining accuracy. RIsearch achieves a speed improvement of at least 2.4x compared to RNAplex, the currently fastest method for searching near-complementary regions. Using RIsearch as a pre-filter in genome-wide screens reduces the number of binding site candidates reported by miRNA target prediction programs by up to 70%.

Topic

Bioinformatics;Sequence alignment

Detail

  • Operation: Sequence alignment analysis

  • Software interface: Command-line user interface

  • Language: -

  • License: GNU General Public License along with RIsearch

  • Cost: Free

  • Version name: 1.2

  • Credit: Danish Council for Independent Research (Technology and Production Sciences), The Danish Council for Strategic Research (Programme Commission on Strategic Growth Technologies), the Danish Center for Scientific Computing.

  • Input: -

  • Output: -

  • Contact: wenzel@rth.dk

  • Collection: -

  • Maturity: -

Publications

  • RIsearch: fast RNA-RNA interaction search using a simplified nearest-neighbor energy model.
  • Wenzel A, et al. RIsearch: fast RNA-RNA interaction search using a simplified nearest-neighbor energy model. RIsearch: fast RNA-RNA interaction search using a simplified nearest-neighbor energy model. 2012; 28:2738-46. doi: 10.1093/bioinformatics/bts519
  • https://doi.org/10.1093/bioinformatics/bts519
  • PMID: 22923300
  • PMC: PMC3476332
  • RIsearch2: suffix array-based large-scale prediction of RNA-RNA interactions and siRNA off-targets.
  • Alkan F, et al. RIsearch2: suffix array-based large-scale prediction of RNA-RNA interactions and siRNA off-targets. RIsearch2: suffix array-based large-scale prediction of RNA-RNA interactions and siRNA off-targets. 2017; 45:e60. doi: 10.1093/nar/gkw1325
  • https://doi.org/10.1093/nar/gkw1325
  • PMID: 28108657
  • PMC: PMC5416843

Download and documentation

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