Concepts and Introduction to RNA Bioinformatics

  • Jan Gorodkin
  • Ivo L. Hofacker
  • Walter L. Ruzzo
Part of the Methods in Molecular Biology book series (MIMB, volume 1097)


RNA bioinformatics and computational RNA biology have emerged from implementing methods for predicting the secondary structure of single sequences. The field has evolved to exploit multiple sequences to take evolutionary information into account, such as compensating (and structure preserving) base changes. These methods have been developed further and applied for computational screens of genomic sequence. Furthermore, a number of additional directions have emerged. These include methods to search for RNA 3D structure, RNA–RNA interactions, and design of interfering RNAs (RNAi) as well as methods for interactions between RNA and proteins.

Here, we introduce the basic concepts of predicting RNA secondary structure relevant to the further analyses of RNA sequences. We also provide pointers to methods addressing various aspects of RNA bioinformatics and computational RNA biology.

Key words

Mutual information RNA folding RNA prediction evaluation RNA secondary structure RNA structure prediction 



This work is supported by the Danish Council for Independent Research (Technology and Production Sciences), the Danish Council for Strategic Research (Programme Commission on Strategic Growth Technologies), as well as the Danish Center for Scientific Computing.


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Copyright information

© Springer Science+Business Media New York 2014

Authors and Affiliations

  • Jan Gorodkin
    • 1
  • Ivo L. Hofacker
    • 1
    • 2
  • Walter L. Ruzzo
    • 3
    • 4
    • 5
  1. 1.Center for non-coding RNA in Technology and Health, IKVHUniversity of CopenhagenFrederiksberg CDenmark
  2. 2.Department of Theoretical ChemistryUniversity of ViennaViennaAustria
  3. 3.Department of Computer Science and EngineeringUniversity of WashingtonSeattleUSA
  4. 4.Department of Genome SciencesUniversity of WashingtonSeattleUSA
  5. 5.Fred Hutchinson Cancer Research CenterSeattleUSA

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