title: Computational prediction of RNA-RNA interactions.
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.
authors.affiliation: Lehrstuhl fur Bioinformatik, Albert-Ludwigs-Universitat, Freiburg, Germany.
authors.forename: Rolf
authors.initials: R
authors.lastname: Backofen
mesh_terms: D000465:Algorithms; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods*; D023281:Genomics / Q000379:methods*; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry* / Q000235:genetics
chemical_list: D012313:RNA