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

Overview

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 ...

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Overview

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.

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Product Details

  • ISBN-13: 9781627037082
  • Publisher: Springer-Verlag New York, LLC
  • Publication date: 4/30/2014
  • Series: Methods in Molecular Biology Series , #1097
  • Edition description: 2014
  • Pages: 533
  • Product dimensions: 7.10 (w) x 10.10 (h) x 1.30 (d)

Table of Contents

1. Concepts and Introduction to RNA Bioinformatics

Jan Gorodkin, Ivo L. Hofacker and Walter L. Ruzzo

2. The Principles of RNA Structure Architecture

Christian Zwieb

3. The Determination of RNA Folding Nearest Neighbor Parameters

Mirela Andronescu, Anne Condon, Douglas H. Turner, and David H. Mathews

4. Energy Directed RNA Structure Prediction

Ivo L. Hofacker

5. Introduction to Stochastic Context Free Grammars

Robert Giegerich

6. An Introduction to RNA Databases

Marc P. Hoeppner, Lars E. Barquist, and Paul P. Gardner

7. Energy-based RNA Consensus Secondary Structure Prediction in Multiple Sequence

Alignments

Stefan Washietl and Stephan H. Bernhart and Manolis Kellis

8. SCFGs in RNA Secondary Structure Prediction: A Hands-on Approach

Zsuzsanna S¨uk¨osd, Ebbe S. Andersen and Rune Lyngsø

9. Annotating Functional RNAs in Genomes using Infernal

Eric P. Nawrocki

10. Class-specific Prediction of ncRNAs

Peter F. Stadler

11. Abstract Shape Analysis of RNA

Stefan Janssen and Robert Giegerich

12. Introduction to RNA Secondary Structure Comparison

Stefanie Schirmer, Yann Ponty, and Robert Giegerich

13. RNA Structural Alignments, Part I: Sankoff Based Approaches for Structural Alignments

Jakob Hull Havgaard and Jan Gorodkin

14. RNA Structural Alignments, Part II: Non-Sankoff Approaches for Structural Alignments

Kiyoshi Asai and Michiaki Hamada

15. De novo Discovery of Structured ncRNA Motifs in Genomic Sequences

Walter L. Ruzzo and Jan Gorodkin

16. Phylogeny and Evolution of RNA Structure

Tanja Gesell and Peter Schuster

17. The Art of Editing RNA Structural Alignments

Ebbe Sloth Andersen

18. Automated Modeling of RNA 3D Structure

Kristian Rother, Magdalena Rother, Pawel Skiba, Janusz M. Bujnicki

19. Computational Prediction of RNA-RNA Interactions

Rolf Backofen

20. Computational Prediction of microRNA Genes

Jana Hertel, David Langenberger, and Peter F. Stadler

21. MicroRNA Target Finding by Comparative Genomics

Robin C. Friedman and Christopher B. Burge

22. Bioinformatics of siRNA Design

Hakim Tafer

23. RNA-protein Interactions: An Overview

Angela Re, Tejal Joshi, Eleonora Kulberkyte, Quaid Morris and Christopher T Workman

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