@article{Backofen-Compu_Predi_RNA-2014,
author = {Backofen, Rolf},
title = {Computational {Prediction} of {RNA}-{RNA} {Interactions}},
journal = {Methods Mol Biol},
year = {2014},
doi = {10.1007/978-1-62703-709-9_19},
volume = {1097},
user = {backofen},
pmid = {24639170},
pages = {417-35},
number = {},
issn = {1064-3745},
abstract = {We describe different tools and approaches for RNA-RNA 
            interaction prediction. Recognition of ncRNA targets is 
            predominantly governed by two principles, namely the 
            stability of the duplex between the two interacting RNAs and 
            the internal structure of both mRNA and ncRNA. Thus, 
            approaches can be distinguished into different major 
            categories depending on how they consider inter- and 
            intramolecular structure. The first class completely 
            neglects the internal structure and measures only the 
            stability of the duplex. The second class of approaches 
            abstracts from specific intramolecular structures and uses 
            an ensemble-based approach to calculate the effect of 
            internal structure on a putative binding site, thus 
            measuring the accessibility of the binding sites.Since 
            accessibility-based approaches can handle only one 
            continuous interaction site, two addition types of 
            approaches were introduced which predict a joint structure 
            for the interacting RNAs. Since this problem is NP-complete, 
            the approaches can handle only a restricted class of joint 
            structures. The first are co-folding approaches, which 
            predict a joint structure that is nested when the both 
            sequences are concatenated. The last and most complex class 
            of approaches impose only the restriction that they discard 
            zipper-like structures. Finally, we will discuss the use of 
            conservation information in RNA-target prediction.}
}