European Biophysics Journal

, Volume 25, Issue 2, pp 115–130

Algorithm independent properties of RNA secondary structure predictions

  • Manfred Tacker
  • Peter F. Stadler
  • Erich G. Bornberg-Bauer
  • Ivo L. Hofacker
  • P. Schuster
ARTICLE

DOI: 10.1007/s002490050023

Cite this article as:
Tacker, M., Stadler, P., Bornberg-Bauer, E. et al. Eur Biophys J (1996) 25: 115. doi:10.1007/s002490050023

Abstract

Algorithms predicting RNA secondary structures based on different folding criteria – minimum free energies (mfe), kinetic folding (kin), maximum matching (mm) – and different parameter sets are studied systematically. Two base pairing alphabets were used: the binary GC and the natural four-letter AUGC alphabet. Computed structures and free energies depend strongly on both the algorithm and the parameter set. Statistical properties, such as mean number of base pairs, mean numbers of stacks, mean loop sizes, etc., are much less sensitive to the choice of parameter set and even of algorithm. Some features of RNA secondary structures, such as structure correlation functions, shape space covering and neutral networks, seem to depend only on the base pairing logic (GC or AUGC alphabet).

Key words Kinetic folding Minimun free energy structures RNA secondary structures Sequence structure relations 

Copyright information

© Springer-Verlag Berlin Heidelberg 1996

Authors and Affiliations

  • Manfred Tacker
    • 4
  • Peter F. Stadler
    • 1
  • Erich G. Bornberg-Bauer
    • 5
  • Ivo L. Hofacker
    • 6
  • P. Schuster
    • 1
  1. 1.Institut für Theoretische Chemie, Universität Wien, Währingerstrasse 17, A-1090 Wien, Austria (Fax: +43 1 40480 660; e-mail: pkstbi.univie.ac.at)AT
  2. 2.Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USAUS
  3. 3.Abteilung Molekulare Evolutionsbiologie, Institut für Molekulare Biotechnologie e.V., Beutenbergstrasse 11, Postfach 100813, D-07708 Jena, GermanyDE
  4. 4.Österreichisches Verpackungsinstitut für Lebens- und Genußmittel, Franz-Grill-Strasse 5, A-1030 Wien, AustriaAT
  5. 5.Abteilung für Theoretische Bioinformatik, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 280, D-69120 Heidelberg, GermanyDE
  6. 6.Beckman Institute, 495 N Mathews, Urbana, Il 61801, USAUS