Tuyển tập các báo cáo nghiên cứu về sinh học được đăng trên tạp chí y học Molecular Biology cung cấp cho các bạn kiến thức về ngành sinh học đề tài: Fast prediction of RNA-RNA interaction. | Salari et al. Algorithms for Molecular Biology 2010 5 5 http content 5 1 5 AMR ALGORITHMS FOR MOLECULAR BIOLOGY RESEARCH Open Access Fast prediction of RNA-RNA interaction Raheleh Salari 1 Rolf Backofen2 S Cenk Sahinalp1 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. Background Regulatory non-coding RNAs ncRNAs play an important role in gene regulation. Studies on both prokaryotic and eukaryotic cells show that such ncRNAs usually bind to their target mRNA to regulate the translation of corresponding genes. Many regulatory RNAs such as microRNAs and small interfering RNAs miRNAs siR-NAs are very short and have full sequence complementarity to the targets. However some of the regulatory antisense RNAs are relatively long and are not fully complementary to their target sequences. They exhibit their regulatory functions by establishing .
