RIsearch2

Brief background

Regulatory, non-coding RNAs often function by duplex formation with other RNAs. It is known that these RNA–RNA interactions are built up by complementary base pairings between interacting RNAs and high level of complementarity between two RNA sequences is a powerful predictor of such interactions. RIsearch2 is a large-scale RNA–RNA interaction prediction tool that enables quick localisation of potential near-complementary RNA–RNA interactions between given query and target sequences. Using a seed-and-extend framework based on suffix arrays, it can perform fast discovery of candidate RNA–RNA interactions on genome/transcriptome-wide scale. Like its predecessor RIsearch, RIsearch2 also uses a modified Smith-Waterman-Gotoh algorithm based on di-nucleotides to approximate nearest-neighbor energy parameters. However, instead of performing the computation with whole sequences, RIsearch2 focuses on perfect-complementary seed regions and extends them on both-ends. User-defined seed and extension constraints makes RIsearch2 applicable to all kinds of RNA-RNA interaction predictions. For instance, our siRNA off-target discovery pipeline, published together with the RIsearch2 method, enables accurate prediction of siRNA off-targets and computation of siRNA off-targeting potential on given transcriptome data.

Get software

You can download the RIsearch2 software below.
To download the siRNA off-target discovery pipeline that is published together with RIsearch2, follow the link below.
For the predecessor RIsearch, please visit its own page by clicking here.

Installation

After downloading, unpack and follow the instructions given in the README and INSTALL files.
tar -xzvf RIsearch-2.0.tar.gz
cd RIsearch-2.0
less README
less INSTALL
...
If you followed the INSTALL instructions successfully, this should create a standalone executable 'risearch2.x' in the bin folder.
To test if you have successfully installed the software, please try our Test Suite provided within the software package.
cd RIsearch-2.0/test_suite
less README
...
After testing, for more convenient use, add the installation folder to PATH or copy the binary to a location that is in $PATH, i.e.
cp RIsearch-2.0/bin/risearch2.x /usr/local/bin/.

Usage

  • For full details about how to use the RIsearch2 software, please read the Manual.pdf distributed with the code package.
  • For full details about how to use the siRNA off-target discovery pipeline, please read the Manual.pdf distributed with the code package.

Citation

When using this software, please cite:

RIsearch2: suffix array-based large-scale prediction of RNA–RNA interactions and siRNA off-targets
Alkan F, Wenzel A, Palasca O, Kerpedjiev P, Rudebeck A, Stadler PF, Hofacker IL, Gorodkin J Nucleic Acids Res (2017) 45 (8): e60
[ PubMed | Paper | Software ]

RIsearch: fast RNA–RNA interaction search using a simplified nearest-neighbor energy model
Wenzel A, Akbaşli E, Gorodkin J Bioinformatics 2012, 28(21):2738-2746
[ PubMed | Paper | Software ]


Contact

ferro@rth.dk