Journal of Mathematical Biology

, Volume 56, Issue 1–2, pp 129–144 | Cite as

Variations on RNA folding and alignment: lessons from Benasque

  • Athanasius F. Bompfünewerer
  • Rolf Backofen
  • Stephan H. Bernhart
  • Jana Hertel
  • Ivo L. Hofacker
  • Peter F. Stadler
  • Sebastian Will


Dynamic programming algorithms solve many standard problems of RNA bioinformatics in polynomial time. In this contribution we discuss a series of variations on these standard methods that implement refined biophysical models, such as a restriction of RNA folding to canonical structures, and an extension of structural alignments to an explicit scoring of stacking propensities. Furthermore, we demonstrate that a local structural alignment can be employed for ncRNA gene finding. In this context we discuss scanning variants for folding and alignment algorithms.


RNA folding Secondary structure alignment Dynamic programming 

Mathematics Subject Classification (2000)

90C27 90C90 92C40 


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Copyright information

© Springer-Verlag 2007

Authors and Affiliations

  • Athanasius F. Bompfünewerer
    • 1
    • 2
  • Rolf Backofen
    • 3
  • Stephan H. Bernhart
    • 2
  • Jana Hertel
    • 4
  • Ivo L. Hofacker
    • 2
  • Peter F. Stadler
    • 2
    • 4
    • 5
  • Sebastian Will
    • 3
  1. 1.Zentralfriedhof WienWienAustria
  2. 2.Department of Theoretical ChemistryUniversity of ViennaWienAustria
  3. 3.Bioinformatics Group, Department of Computer ScienceUniversity of FreiburgFreiburgGermany
  4. 4.Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for BioinformaticsUniversity of LeipzigLeipzigGermany
  5. 5.Santa Fe InstituteSanta FeUSA

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