RNA Sequence, Structure and Function: Computational and Bioinformatic Methods

         

Jan Gorodkin and Walter L Ruzzo, editors

Methods in Molecular Biology, Humana Press (Springer Protocols)

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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.

Contents

Preface
Jan Gorodkin and Walter L Ruzzo

Chapter 1: Concepts and Introduction to RNA Bioinformatics
Jan Gorodkin, Ivo L Hofacker and Walter L Ruzzo

Chapter 2: Principles of RNA structure
Christian Zwieb

Chapter 3: The Determination of RNA Folding Nearest Neighbor Parameters
Mirela Andronescu, Anne Condon, Doug Turner and David Mathews

Chapter 4: Energy directed RNA struture prediction
Ivo L. Hofacker

Chapter 5: Introduction to Stochastic Context-Free Grammars
Robert Giegerich

Chapter 6: An introduction to RNA databases
Marc Hoeppner, Lars E. Barquist and Paul Gardner

Chapter 7: Energy based RNA structure prediction from multiple alignments
Stefan Washietl, Stephan H Bernhart and Manolis Kellis

Chapter 8: SCFGs for RNA structure prediction: a hands-on approach
Zsuzsanna Sukosd, Ebbe S Andersen and Rune Lyngsø

Chapter 9: Annotating functional RNAs in genomes using Infernal
Eric Nawrocki

Chapter 10: Class specific prediction of ncRNAs
Peter Stadler

Chapter 11: RNA structure analysis and motif search with abstract shapes
Stefan Janssen and Robert Giegerich

Chapter 12: Introduction to RNA secondary structure comparison
Stefanie Schirmer, Yann Ponty and Robert Giegerich

Chapter 13 RNA structural alignments, Part I: Sankoff based approaches for structural alignments
Jakob Hull Havgaard and Jan Gorodkin

Chapter 14 RNA structural alignments, Part II: Non-Sankoff approaches for Structural alignments
Kiyoshi Asai and Michiaki Hamada

Chapter 15 De novo ncRNA gene and RNA structure motif search
Larry Ruzzo and Jan Gorodkin

Chapter 16 Phylogeny and evolution of RNA structure
Tanja Gesell and Peter Schuster

Chapter 17 The art of editing RNA structural alignments
Ebbe S Andersen

Chapter 18 Template-based modeling of RNA 3D structure
Kristian Rother, Magdalena Rother, Pawel Skiba and Janusz M. Bujnicki

Chapter 19: Computational Prediction of RNA-RNA interactions
Rolf Backofen

Chapter 20 Computational prediction of microRNA genes
Jana Hertel, David Langenberger and Peter Stadler

Chapter 21 MicroRNA target finding by comparative genomics
Robin Friedman and Chris Burge

Chapter 22 Bioinformatics of siRNA design
Hakim Tafer

Chapter 23 RNA-protein interactions
Angela Re, Tejal Joshi, Eleonora Kulberkyte, Quaid Morris and Christopher Workman