Comparative RNA Genomics

  • Rolf Backofen
  • Jan Gorodkin
  • Ivo L. Hofacker
  • Peter F. StadlerEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1704)


Over the last two decades it has become clear that RNA is much more than just a boring intermediate in protein expression. Ancient RNAs still appear in the core information metabolism and comprise a surprisingly large component in bacterial gene regulation. A common theme with these types of mostly small RNAs is their reliance of conserved secondary structures. Large scale sequencing projects, on the other hand, have profoundly changed our understanding of eukaryotic genomes. Pervasively transcribed, they give rise to a plethora of large and evolutionarily extremely flexible noncoding RNAs that exert a vastly diverse array of molecule functions. In this chapter we provide a—necessarily incomplete—overview of the current state of comparative analysis of noncoding RNAs, emphasizing computational approaches as a means to gain a global picture of the modern RNA world.

Key words

Long noncoding RNA RNA secondary structure Chromatin Alternative splicing Evolution 



This work was funded in part by the German Federal Ministry of Education and Research (BMBF; 031A538B) within the German Network for Bioinformatics Infrastructure (de.NBI), the Deutsche Forschungsgemeinschaft (DFG; BA 2168/11-2, BA2168/3-3, and STA 850/19) within the Priority Programme SPP 1738, the Innovation Fund Denmark (0603-00320B, 5163-00010B), The Danish Council for Independent Research (DFF-4005-00443).


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Copyright information

© Springer Science+Business Media LLC 2018

Authors and Affiliations

  • Rolf Backofen
    • 1
    • 2
  • Jan Gorodkin
    • 2
  • Ivo L. Hofacker
    • 2
    • 3
    • 4
  • Peter F. Stadler
    • 5
    • 2
    • 3
    • 6
    • 7
    • 8
    Email author
  1. 1.Bioinformatics Group, Department of Computer ScienceUniversity of FreiburgD-79110 FreiburgGermany
  2. 2.Center for non-coding RNA in Technology and Health, Department of Veterinary and Animal SciencesUniversity of CopenhagenDK-1870 Frederiksberg CDenmark
  3. 3.Institute for Theoretical ChemistryUniversity of ViennaA-1090 WienAustria
  4. 4.Bioinformatics and Computational Biology Research GroupUniversity of ViennaA-1090 ViennaAustria
  5. 5.Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for BioinformaticsUniversity of LeipzigD-04107 LeipzigGermany
  6. 6.Max Planck Institute for Mathematics in the SciencesD-04103 LeipzigGermany
  7. 7.Fraunhofer Institute for Cell Therapy and ImmunologyD-04103 LeipzigGermany
  8. 8.Santa Fe InstituteSanta FeUSA

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