Regulatory, non-coding RNAs often function by duplex formation with other RNAs. Additionally, RNAs can be found in complex in which proteins facilitate DNA opening and allow the RNA to bind to the DNA. It is known that RNA–RNA, RNA-DNA, and DNA-DNA interactions are built up by complementary base pairings and high level of complementarity between two RNA/DNA sequences is a powerful predictor of such interactions. The RIsearch package includes the RIsearch2 tool for large-scale RNA–RNA, RNA-DNA, and DNA-DNA interaction prediction tool and its predecessor RIsearch1. Both tools enable quick localisation of potential near-complementary interactions between given query and target sequences. Both RIsearch1 and RIsearch2 use a modified Smith-Waterman-Gotoh algorithm based on di-nucleotides to approximate nearest-neighbor energy parameters. However, while RIsearch1 performs the computation with whole sequences, RIsearch2 focuses on perfect-complementary seed regions and extends them on both-ends using a seed-and-extend framework based on suffix arrays. The usage of suffix arrays in RIsearch2 allows to perform fast discovery of interactions between RNA-RNA, RNA-DNA, and DNA-DNA on genome/transcriptome-wide scale. User-defined seed and extension constraints makes RIsearch2 applicable to all kinds of interaction predictions (eg. siRNA and Cas9-gRNA off-target predicitons).


The installation now includes both RIsearch1 and RIsearch2 in a combined package as a conda install or as a source code package.


The easiest way to obtain and install RIsearch is via Conda:

conda install -c rthtools risearch

On old architectures we recommend to run the installation as follows:

conda install -c rthtools -c conda-forge risearch


Alternatively, RIsearch can be downloaded below. After download, unpack the file and follow the instructions given in the README and INSTALL files under RIsearch-1.2/RIsearch1 and RIsearch-1.2/Risearch2, respectively.

The current version of RIsearch is 1.2.


For full details about how to use the RIsearch1 and RIsearch2, please read the corresponding Manual.pdf distributed with the code packages or download it below:

siRNA pipeline

To download the siRNA off-target discovery pipeline that is published together with RIsearch2, follow the link below.

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


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 AF, Stadler PF, Hofacker IL, Gorodkin J* Nucleic Acids Res. 2017 May 5;45(8):e60
[ PubMed | Paper | Software ]

RIsearch: fast RNA-RNA interaction search using a simplified nearest-neighbor energy model

Wenzel A, Akbasli E, Gorodkin J* Bioinformatics. 2012 Nov 1;28(21):2738-46. Epub 2012 Aug 24
[ PubMed | Paper | Software ]


In case of problems or bug reports, please contact software+risearch@rth.dk