@Article{Salari:Backofen:Sahinalp:Fast_predi_RNA:2010,
  author =	 {Salari, Raheleh and Backofen, Rolf and Sahinalp, S. Cenk},
  title =	 {Fast prediction of {RNA}-{RNA} interaction},
  journal =	 {Algorithms Mol Biol},
  year =	 {2010},
  volume =	 {5},
  number =	 {},
  pages =	 {5},
  issn =         {1748-7188},
  user =	 {arichter},
  pmid =	 {20047661},
  doi = 	 {10.1186/1748-7188-5-5},
  abstract =	 {ABSTRACT: BACKGROUND: Regulatory antisense RNAs are a class 
                  of ncRNAs that regulate gene expression by prohibiting the 
                  translation of an mRNA by establishing stable interactions 
                  with a target sequence. There is great demand for efficient 
                  computational methods to predict the specific interaction 
                  between an ncRNA and its target mRNA(s). There are a number 
                  of algorithms in the literature which can predict a variety 
                  of such interactions - unfortunately at a very high 
                  computational cost. Although some existing target prediction 
                  approaches are much faster, they are specialized for 
                  interactions with a single binding site. METHODS: In this 
                  paper we present a novel algorithm to accurately predict the 
                  minimum free energy structure of RNA-RNA interaction under 
                  the most general type of interactions studied in the 
                  literature. Moreover, we introduce a fast heuristic method 
                  to predict the specific (multiple) binding sites of two 
                  interacting RNAs. RESULTS: We verify the performance of our 
                  algorithms for joint structure and binding site prediction 
                  on a set of known interacting RNA pairs. Experimental 
                  results show our algorithms are highly accurate and 
                  outperform all competitive approaches.}
}