RNA Sequence, Structure, and Function: Computational and Bioinformatic Methods

The existence of genes for RNA molecules not coding for proteins (ncRNAs) has been recognized since the 1950's, but until recently, aside from the critically important ribosomal and transfer RNA genes, most focus has been on protein coding genes.  However, a long series of striking discoveries, from RNA's ability to carry out catalytic function, to discovery of riboswitches, microRNAs and other ribo-regulators performing critical tasks in essentially all living organisms, has created a burgeoning interest in this primordial component of the biosphere.  However, the structural characteristics and evolutionary constraints on RNA molecules are very different from those of proteins, necessitating development of a completely new suite of informatic tools to address these challenges. In RNA Sequence, Structure, Function: Computational and Bioinformatic Methods, expert researchers in the field describe a substantial and relevant fraction of these methodologies from both practical and computational/algorithmic perspectives. Focusing on both of these directions addresses both the biologist interested in knowing more about RNA bioinformatics as well as the bioinformaticist interested in more detailed aspects of the algorithms.  Written in the highly successful Methods in Molecular Biology series format, the chapters include the kind of detailed description and implementation advice that is crucial for getting optimal results.

Thorough and intuitive, RNA Sequence, Structure, Function: Computational and Bioinformatic Methods aids scientists in continuing to study key methods and principles of RNA bioinformatics.

• De novo search for structured RNAs
• Homology search
• RNA 3D Structure
• RNA 3D modeling
• RNA Bioinformatics
• RNA databases
• RNA folding
• RNA folding parameters
• RNA interactions
• RNA secondary structure
• The energy model
• class-specific ncRNAs
• genomic annotation
• probabilistic modeling
• siRNA design
• stochastic context-free grammars
• structural alignments of RNAs

From the book reviews:

“This book on RNA structure and function is suitable for both graduate and post-graduate students as well as established researchers. … the book is also a valuable review of the state of the art of hot topics on cutting edge directions of research. In addition, the value of each chapter is enriched by an extensive set of references of recent yet established papers, offering a reliable starting point for literature on each research topic.” (Irina Ioana Mohorianu, zbMATH 1307.92008, 2015)

• Center for non-coding RNA in Technology and Health, IKVH University of Copenhagen, Frederiksberg, Denmark

  Jan Gorodkin

• University of Washington Dept. Computer Science & Engineering, Seattle, USA

  Walter L. Ruzzo

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