This Article 
   
 Share 
   
 Bibliographic References 
   
 Add to: 
 
Digg
Furl
Spurl
Blink
Simpy
Google
Del.icio.us
Y!MyWeb
 
 Search 
   
A New Distance for High Level RNA Secondary Structure Comparison
January-March 2005 (vol. 2 no. 1)
pp. 3-14
We describe an algorithm for comparing two RNA secondary structures coded in the form of trees that introduces two new operations, called node fusion and edge fusion, besides the tree edit operations of deletion, insertion, and relabeling classically used in the literature. This allows us to address some serious limitations of the more traditional tree edit operations when the trees represent RNAs and what is searched for is a common structural core of two RNAs. Although the algorithm complexity has an exponential term, this term depends only on the number of successive fusions that may be applied to a same node, not on the total number of fusions. The algorithm remains therefore efficient in practice and is used for illustrative purposes on ribosomal as well as on other types of RNAs.

[1] D. Bouthinon and H. Soldano, “A New Method to Predict the Consensus Secondary Structure of a Set of Unaligned RNA Sequences,” Bioinformatics, vol. 15, no. 10, pp. 785-798, 1999.
[2] J.W. Brown, “The Ribonuclease P Database,” Nucleic Acids Research, vol. 24, no. 1, p. 314, 1999.
[3] N. el Mabrouk and F. Lisacek, “and Very Fast Identification of RNA Motifs in Genomic DNA. Application to tRNA Search in the Yeast Genome,” J. Molecular Biology, vol. 264, no. 1, pp. 46-55, 1996.
[4] I. Hofacker, “The Vienna RNA Secondary Structure Server,” 2003.
[5] I. Hofacker, W. Fontana, P.F. Stadler, L. Sebastian Bonhoeffer, M. Tacker, and P. Schuster, “Fast Folding and Comparison of RNA Secondary Structures,” Monatshefte für Chemie, vol. 125, pp. 167-188, 1994.
[6] M. Höchsmann, T. Töller, R. Giegerich, and S. Kurtz, “Local Similarity in RNA Secondary Structures,” Proc. IEEE Computer Soc. Conf. Bioinformatics, p. 159, 2003.
[7] M. Höchsmann, B. Voss, and R. Giegerich, “Pure Multiple RNA Secondary Structure Alignments: A Progressive Profile Approach,” IEEE/ACM Trans. Computational Biology and Bioinformatics, vol. 1, no. 1, pp. 53-62, 2004.
[8] T. Winkelmans, J. Wuyts, Y. Van de Peer, and R. De Wachter, “The European Database on Small Subunit Ribosomal RNA,” Nucleic Acids Research, vol. 30, no. 1, pp. 183-185, 2002.
[9] T. Jiang, L. Wang, and K. Zhang, “Alignment of Trees— An Alternative to Tree Edit,” Proc. Fifth Ann. Symp. Combinatorial Pattern Matching, pp. 75-86, 1994.
[10] F. Lisacek, Y. Diaz, and F. Michel, “Automatic Identification of Group I Intron Cores in Genomic DNA Sequences,” J. Molecular Biology, vol. 235, no. 4, pp. 1206-1217, 1994.
[11] B. Shapiro, “An Algorithm for Multiple RNA Secondary Structures,” Computer Applications in the Biosciences, vol. 4, no. 3, pp. 387-393, 1988.
[12] B.A. Shapiro and K. Zhang, “Comparing Multiple RNA Secondary Structures Using Tree Comparisons,” Computer Applications in the Biosciences, vol. 6, no. 4, pp. 309-318, 1990.
[13] K.-C. Tai, “The Tree-to-Tree Correction Problem,” J. ACM, vol. 26, no. 3, pp. 422-433, 1979.
[14] K. Zhang and D. Shasha, “Simple Fast Algorithms for the Editing Distance between Trees and Related Problems,” SIAM J. Computing, vol. 18, no. 6, pp. 1245-1262, 1989.
[15] M. Zuker, “Mfold Web Server for Nucleic Acid Folding and Hybridization Prediction,” Nucleic Acids Research, vol. 31, no. 13, pp. 3406-3415, 2003.

Index Terms:
Tree comparison, edit operation, distance, RNA, secondary structure.
Citation:
Julien Allali, Marie-France Sagot, "A New Distance for High Level RNA Secondary Structure Comparison," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 2, no. 1, pp. 3-14, Jan.-March 2005, doi:10.1109/TCBB.2005.2
Usage of this product signifies your acceptance of the Terms of Use.