Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics

Reeder J, Giegerich R (2004)
BMC Bioinformatics 5(1): 104.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
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DOI
URN
urn:nbn:de:0070-pub-17737588
Autor*in
Reeder, Jens; Giegerich, RobertUniBi
Einrichtung
Centrum für Biotechnologie > Institut für Bioinformatik
Centrum für Biotechnologie > Arbeitsgruppe R. Giegerich
Technische Fakultät > AG Praktische Informatik
Abstract / Bemerkung
Background: The general problem of RNA secondary structure prediction under the widely used thermodynamic model is known to be NP-complete when the structures considered include arbitrary pseudoknots. For restricted classes of pseudoknots, several polynomial time algorithms have been designed, where the O(n6)time and O(n4) space algorithm by Rivas and Eddy is currently the best available program. Results: We introduce the class of canonical simple recursive pseudoknots and present an algorithm that requires O(n4) time and O(n2) space to predict the energetically optimal structure of an RNA sequence, possible containing such pseudoknots. Evaluation against a large collection of known pseudoknotted structures shows the adequacy of the canonization approach and our algorithm. Conclusions: RNA pseudoknots of medium size can now be predicted reliably as well as efficiently by the new algorithm.
Erscheinungsjahr
2004
Zeitschriftentitel
BMC Bioinformatics
Band
5
Ausgabe
1
Art.-Nr.
104
ISSN
1471-2105
Page URI
https://pub.uni-bielefeld.de/record/1773758

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Reeder J, Giegerich R. Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics. BMC Bioinformatics. 2004;5(1): 104.
Reeder, J., & Giegerich, R. (2004). Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics. BMC Bioinformatics, 5(1), 104. https://doi.org/10.1186/1471-2105-5-104
Reeder, Jens, and Giegerich, Robert. 2004. “Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics”. BMC Bioinformatics 5 (1): 104.
Reeder, J., and Giegerich, R. (2004). Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics. BMC Bioinformatics 5:104.
Reeder, J., & Giegerich, R., 2004. Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics. BMC Bioinformatics, 5(1): 104.
J. Reeder and R. Giegerich, “Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics”, BMC Bioinformatics, vol. 5, 2004, : 104.
Reeder, J., Giegerich, R.: Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics. BMC Bioinformatics. 5, : 104 (2004).
Reeder, Jens, and Giegerich, Robert. “Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics”. BMC Bioinformatics 5.1 (2004): 104.
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