Fast Prediction of RNA-RNA Interaction

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. 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. We verify the performance of our algorithms for joint structure and binding site p...

• Type: Conference
• Year: 2009
• Where: WABI
• Authors: Raheleh Salari, Rolf Backofen, Süleyman Cenk Sahinalp
• Keywords: Algorithms, Binding Site, Regulatory Antisense Rnas, Target Prediction Approaches, WABI 2009