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RNA bioinformatics. (English) Zbl 1318.92003
Methods in Molecular Biology 1269. New York, NY: Humana Press/Springer (ISBN 978-1-4939-2290-1/hbk; 978-1-4939-2291-8/ebook). xii, 415 p. (2015).
This text is a timely book that overviews the state of art of methodological approaches for the analysis of RNA data, from the prediction of its secondary or tertiary structure to the parsing of massive RNAseq data. The book is structured in three parts. The first presents approaches for the prediction and understanding of RNA structures. The second is focused on the analysis of high throughput RNA sequencing data and the third presents web resources for RNA data analysis.
The first part commences with an overview of free energy minimization approaches for the prediction of secondary RNA structure such as RNAfold and the McCaskill method. Next, the authors introduce certain methodological details required for predicting the structures, the RNA deleterious mutations and their use for computational RNA design. The second chapter focuses on an alternative approach for predicting secondary structures, one based on multiple alignments. Starting with an example which highlights the differences between the two methods, the author continues with an overview of commonly used tools for structure prediction from aligned sequences. Next, methods based on sequence covariation of base pairs and the use of phylogenetic (evolutionary) information are presented in detail. The use of MEG estimators, the choice of probabilistic models $$p(\theta|A)$$ and of the gain functions $$G(\theta,y)$$ are also discussed. The chapter concludes with the formulation of mathematically related problems of predicting RNA-RNA interactions and determining the common joint structure of the two aligned RNA sequences. In the third chapter, a simple protocol for the inference of RNA global pairwise alignments is proposed. Following a brief description of the computational methods which will be used and the corresponding test datasets, the authors proceed with the comparison of the performance of the algorithms and comment the results using examples. The fourth chapter focuses on de novo motif discovery in secondary structures using RNAProfile. The authors describe in detail the algorithm which consists in the selection of candidate regions and, using a heuristic approach, the identification of motifs. An example run of the tool is also included together with a description of the parameters which are involved. The chapter concludes with several examples. The fifth chapter focuses on the drawing and editing of RNA secondary structures. Commencing with an outline of objectives for RNA visualization and an overview of existing tools, the authors present in detail the commonly used file formats for RNA secondary structures and their typical representations: the linear layout, the circular one, the squiggle plots and the tree layout. The authors also discuss the 3D representation of pseudoknots and interactions. In the sixth chapter, the authors discuss the prediction and modelling of RNA 3D structures. Starting with the classification of base pairing interactions, the authors focus next on the role of RNA motifs and the steps for the prediction of RNA tertiary structure including the prediction of a secondary structure scaffold and the use of an interaction graph with motif insertion. The chapter concludes with an overview of methods of reconstructing tertiary structures from base pairing interaction networks. The last chapter in the first part focuses on the fast prediction of RNA-RNA interactions using a heuristic approach. Following the description of the test dataset, the author describes in detail the algorithm for RNA secondary structure prediction, the RNA-RNA interaction prediction step and the parallelization of the approach to optimize the run time.