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

  • Jan Gorodkin
  • Walter L. Ruzzo

Part of the Methods in Molecular Biology book series (MIMB, volume 1097)

Table of contents

  1. Front Matter
    Pages i-xi
  2. Jan Gorodkin, Ivo L. Hofacker, Walter L. Ruzzo
    Pages 1-31
  3. Christian Zwieb
    Pages 33-43
  4. Mirela Andronescu, Anne Condon, Douglas H. Turner, David H. Mathews
    Pages 45-70
  5. Ivo L. Hofacker
    Pages 71-84
  6. Robert Giegerich
    Pages 85-106
  7. Marc P. Hoeppner, Lars E. Barquist, Paul P. Gardner
    Pages 107-123
  8. Stefan Washietl, Stephan H. Bernhart, Manolis Kellis
    Pages 125-141
  9. Zsuzsanna Sükösd, Ebbe S. Andersen, Rune Lyngsø
    Pages 143-162
  10. Peter F. Stadler
    Pages 199-213
  11. Stefan Janssen, Robert Giegerich
    Pages 215-245
  12. Stefanie Schirmer, Yann Ponty, Robert Giegerich
    Pages 247-273
  13. Walter L. Ruzzo, Jan Gorodkin
    Pages 303-318
  14. Tanja Gesell, Peter Schuster
    Pages 319-378
  15. Ebbe Sloth Andersen
    Pages 379-394
  16. Kristian Rother, Magdalena Rother, Pawel Skiba, Janusz M. Bujnicki
    Pages 395-415
  17. Jana Hertel, David Langenberger, Peter F. Stadler
    Pages 437-456
  18. Robin C. Friedman, Christopher B. Burge
    Pages 457-476
  19. Hakim Tafer
    Pages 477-490
  20. Angela Re, Tejal Joshi, Eleonora Kulberkyte, Quaid Morris, Christopher T. Workman
    Pages 491-521
  21. Back Matter
    Pages 523-533

About this book


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

Editors and affiliations

  • Jan Gorodkin
    • 1
  • Walter L. Ruzzo
    • 2
  1. 1.Center for non-coding RNA in Technology and Health, IKVH University of CopenhagenFrederiksbergDenmark
  2. 2.University of Washington Dept. Computer Science & EngineeringSeattleUSA

Bibliographic information

  • DOI
  • Copyright Information Springer Science+Business Media New York 2014
  • Publisher Name Humana Press, Totowa, NJ
  • eBook Packages Springer Protocols
  • Print ISBN 978-1-62703-708-2
  • Online ISBN 978-1-62703-709-9
  • Series Print ISSN 1064-3745
  • Series Online ISSN 1940-6029
  • Buy this book on publisher's site
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