@Article{Backofen-Compu_Predi_RNA-2014,
  author =	 {Backofen, Rolf},
  title =	 {Computational {Prediction} of {RNA}-{RNA} {Interactions}},
  journal =	 {Methods Mol Biol},
  year =	 {2014},
  volume =	 {1097},
  number =	 {},
  pages =	 {417-35},
  user =	 {backofen},
  pmid =	 {24639170},
  doi = 	 {10.1007/978-1-62703-709-9_19},
  issn = 	 {1064-3745},
  issn = 	 {1940-6029},
  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.}
}