Abstract
A new dynamic programming algorithm with O(n 4) time and O(n 3) space is presented to predict the RNA secondary structure including nested pseudoknots and a subclass of crossed pseudoknots. Compared with the Jens algorithm of O(n 4) time and O(n 2) space, this algorithm can predict more complex pseudoknots. Compared with the Rivas algorithm of O(n 6) time and O(n 4) space, this algorithm has the same power for the planar pseudoknots prediction.
The work is supported by NSFC: 60273032.
Preview
Unable to display preview. Download preview PDF.
Similar content being viewed by others
References
Zuker, M.: Computer prediction of RNA structure. Methods Enzymol 180, 262–288 (1989a)
Schuster, P., Fontana, W., Stadler, P.F., Hofacker, I.L.: From sequences to shapes and back: a case study in RNA secondary structure. Proc. Roy. Soc. ser. B 255, 279–284 (1994)
Rivas, E., Eddy, S.: A dynamic programming algorithm for RNA structure prediction including pseudoknots. J. Mol. Biol. 285, 2053–2068 (1999)
Lyngsφ, R., Pedersen, C.: RNA pseudoknot prediction in energy based models. J. Mol. Biol. 7, 409–428 (2001)
Abrahams, J.P., van der Berg, M., et al.: Prediction of RNA secondary structure, including pseudoknotting, by computer simulation. Nucleic Acids Research 18, 3035–3044 (1990)
Gultyaev, A.P., van Batenburg, F.H., Pleij, C.W.A.: The computer simulation of RNA folding pathways using a genetic algorithm. J. Mol. Biol. 250, 37–51 (1995)
Akutsu, T.: Dynamic programming algorithms for RNA secondary structure prediction with pseudoknots. Discrete Applied Mathematics 104, 45–62 (2000)
Ruan, J., Stormo, G., Zhang, W.: An iterated loop matching approach to the prediction of RNA secondary structures with pseudoknots. Bioinformatics 20, 58–66 (2004)
Hengwu, L., Daming, Z., Shaohan, M.: An impoved algorithm for RNA secondary structure prediction including pseudoknots. In: TCS, Qingdao, pp. 109–111. Computer Science Press, Rockville (2003)
Hengwu, L., Daming, Z., Sun, M.: A new algorithm for RNA secondary structure prediction. In: TCS, Wuhan, pp. 142–144. Computer Science Press, Rockville (2004)
Jens, R., Robert, G.: Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics. BMC Bioinformatics 5, 104 (2004)
PseudoBase homepage http://wwwbio.LeidenUniv.nl/~Batenburg/PKB.htm
Sankoff, D.: Simultaneous solution of the RNA folding, alignment and protosequence problems. SIAM J. Appl. Math. 45, 810–825 (1985)
Gluick, T.C., Draper, D.E.: Thermodynamics of folding a pseudoknotted mRNA fragment. J. Mol. Biol. 241, 246–262 (1999)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2005 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Li, H., Zhu, D. (2005). A New Pseudoknots Folding Algorithm for RNA Structure Prediction. In: Wang, L. (eds) Computing and Combinatorics. COCOON 2005. Lecture Notes in Computer Science, vol 3595. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11533719_12
Download citation
DOI: https://doi.org/10.1007/11533719_12
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-28061-3
Online ISBN: 978-3-540-31806-4
eBook Packages: Computer ScienceComputer Science (R0)