@article{Raden-IntaRNA-handson-2021,
author={Martin Raden and Milad Miladi},
title={How to do {RNA}-{RNA} interaction prediction? A use-case driven handbook using {IntaRNA}},
journal={Methods in Molecular Biology},
year={2022},
issn={1940-6029},
issn={1064-3745},
volume={},
number={},
pages={},
user={mmann},
note={(in production)},
abstract={
Computational prediction of RNA-RNA interactions (RRI) is a central methodology for the specific investigation of inter-molecular RNA interactions and regulatory effects of non-coding RNAs like eukaryotic microRNAs or prokaryotic small RNAs.
Available methods can be classified according to their underlying prediction strategies, each implicating specific capabilities and restrictions often not transparent to the non-expert user.
Within this work, we review seven classes of RRI prediction strategies and discuss advantages and limitations of respective tools, since such knowledge is essential for selecting the right tool in the first place.

Currently, accessibility-based approaches provide the most reliable RRI predictions.
Thus, we discuss how IntaRNA, one of the state-of-the-art accessibility-based tools, can be applied in various use cases of computational RRI prediction.
Detailed hands-on examples both for specific RRI prediction as well as large-scale target prediction are provided to illustrate the flexibility and capabilities of IntaRNA.
Each example uses realistic data from the literature and is accompanied by instructions how to interpret respective results to enable non-expert users to comprehensively understand and utilize IntaRNAs features for RRI predictions.
}
}