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RNA Folding Algorithms with G-Quadruplexes

  • Ronny Lorenz
  • Stephan H. Bernhart
  • Fabian Externbrink
  • Jing Qin
  • Christian Höner zu Siederdissen
  • Fabian Amman
  • Ivo L. Hofacker
  • Peter F. Stadler
Part of the Lecture Notes in Computer Science book series (LNCS, volume 7409)

Abstract

G-quadruplexes are abundant locally stable structural elements in nucleic acids. The combinatorial theory of RNA structures and the dynamic programming algorithms for RNA secondary structure prediction are extended here to incorporate G-quadruplexes using a simple but plausible energy model. With preliminary energy parameters we find that the overwhelming majority of putative quadruplex-forming sequences in the human genome are likely to fold into canonical secondary structures instead.

Keywords

Dynamic programming RNA folding ViennaRNA Package 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • Ronny Lorenz
    • 1
  • Stephan H. Bernhart
    • 2
  • Fabian Externbrink
    • 2
  • Jing Qin
    • 3
  • Christian Höner zu Siederdissen
    • 1
  • Fabian Amman
    • 1
  • Ivo L. Hofacker
    • 1
    • 4
  • Peter F. Stadler
    • 1
    • 2
    • 3
    • 4
    • 5
    • 6
  1. 1.Dept. Theoretical ChemistryUniv. ViennaWienAustria
  2. 2.Dept. Computer Science, and Interdisciplinary Center for BioinformaticsUniv. LeipzigLeipzigGermany
  3. 3.Mathematics in the SciencesMPILeipzigGermany
  4. 4.RTHUniv. CopenhagenFrederiksberg CDenmark
  5. 5.Cell Therapy and ImmunologyFHILeipzigGermany
  6. 6.Santa Fe InstituteSanta FeUSA

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