Fast Prediction of RNA-RNA Interaction

Peer reviewed: 
Yes, item is peer reviewed.
Scholarly level: 
Faculty/Staff
Final version published as: 

Salari et al. Algorithms for Molecular Biology 2010, 5:5
http://www.almob.org/content/5/1/5

Date created: 
2010
Abstract: 

Background: Regulatory antisense RNAs are a class of ncRNAs that regulate gene expression by prohibiting thetranslation of an mRNA by establishing stable interactions with a target sequence. There is great demand forefficient 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 - unfortunatelyat a very high computational cost. Although some existing target prediction approaches are much faster, they arespecialized for interactions with a single binding site.Methods: In this paper we present a novel algorithm to accurately predict the minimum free energy structure ofRNA-RNA interaction under the most general type of interactions studied in the literature. Moreover, we introducea 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 ofknown interacting RNA pairs. Experimental results show our algorithms are highly accurate and outperform allcompetitive approaches.

Language: 
English
Document type: 
Article
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