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: Hierarchical folding of multiple sequence alignments for the prediction of structures and RNA-RNA interactions. | Seemann et al. Algorithms for Molecular Biology 2010 5 22 http content 5 1 22 AMR ALGORITHMS FOR ID MOLECULAR BIOLOGY RESEARCH Open Access Hierarchical folding of multiple sequence alignments for the prediction of structures and RNA-RNA interactions Stefan E Seemann21 Andreas S Richter22 Jan Gorodkin1 and Rolf Backofen 2 Abstract Background Many regulatory non-coding RNAs ncRNAs function through complementary binding with mRNAs or other ncRNAs microRNAs snoRNAs and bacterial sRNAs. Predicting these RNA interactions is essential for functional studies of putative ncRNAs or for the design of artificial RNAs. Many ncRNAs show clear signs of undergoing compensating base changes over evolutionary time. Here we postulate that a non-negligible part of the existing RNA-RNA interactions contain preserved but covarying patterns of interactions. Methods We present a novel method that takes compensating base changes across the binding sites into account. The algorithm works in two steps on two pre-generated multiple alignments. In the first step individual base pairs with high reliability are found using the PETfold algorithm which includes evolutionary and thermodynamic properties. In step two where high reliability base pairs from step one are constrained as unpaired the principle of cofolding is combined with hierarchical folding. The final prediction of intra- and inter-molecular base pairs consists of the reliabilities computed from the constrained expected accuracy scoring which is an extended version of that used for individual multiple alignments. Results We derived a rather extensive algorithm. One of the advantages of our approach in contrast to other RNA-RNA interaction prediction methods is the application of covariance detection and prediction of pseudoknots between intra- and inter-molecular base pairs. As a proof of concept we show an example and discuss the strengths and weaknesses of the approach. Background Predicting RNA-RNA interactions is
