Abstract
RNA pseudoknots are not only important structural elements for forming the tertiary structure, but also responsible for several functions of RNA molecules such as frame-shifting, read-through, and the initiation of translation. There exists no automatic method for drawing RNA pseudoknot structures, and thus representing RNA pseudoknots currently relies on significant amount of manual work. This paper describes the first algorithm for automatically generating a drawing of H-type pseudoknots with RNA secondary structures. Two basic criteria were adopted when designing the algorithm: (1) overlapping of structural elements should be minimized to increase the readability of the drawing, and (2) the whole RNA structure containing pseudoknots as well as the pseudoknots themselves should be recognized quickly and clearly. Experimental results show that this algorithm generates uniform and clear drawings with no edge crossing for all H-type RNA pseudoknots. The algorithm is currently being extended to handle other types of pseudoknots.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Deiman, B.A. L. M., Pleij, C.W.A.: Pseudoknots: A Vital Feature in Viral RNA. Seminars in Virology 8 (1997) 166–175 181
Du, Z., Hoffman, D.W.: An NMR and mutational study of the pseudoknot within the gene 32 mRNA of bacteriophage T2: insights into a family of structurally related RNA pseudoknots. Nucleic Acids Research 25 (1997) 1130–1135 181
Hilbers, C.W., Michiels, P. J.A., Heus, H.A.: New Developments in Structure Determination of Pseudoknots. Biopolymers 48 (1998) 137–153
Han, K., Kim, D., Kim, H.-J.: A vector-based method for drawing RNA secondary structure. Bioinformatics 15 (1999) 286–197 182
Chetouani, F., Monestie, P., Thebault, P., Gaspin, C., Michot, B.: ESSA: an integrated and interactive computer tool for analyzing RNA secondary structure. Nucleic Acids Research 25 (1997) 3514–3522 182
Shapiro, B.A., Maizel, J., Lipkin, L.E., Currey, K., Whitney, C.: Generating nonoverlapping displays of nucleic acid secondary structure. Nucleic Acids Research 12 (1984) 75–88182
Winnepenninckx, B., Van de Peer, Y., Backeljau, T., De Wachter, R.: CARD: A Drawing Tool for RNA Secondary Structure Models. BioTechniques 16 (1995) 1060–1063 182
De Rijk, P., De Wachter, R.: RnaVIz, a program for the visualization of RNA secondary structure. Nucleic Acids Research 25 (1997) 4679–4684
van Batenburg, F.H.D., Gultyaev, A.P., Pleij, C.W.A., Ng, J., Olihoek, J.: PseudoBase: a database with RNA pseudoknots. Nucleic Acids Research 28 (2000) 201–204 185, 193
Gultyaev, A.P., van Batenburg, E. Pleij, C. W.A.: Similarities between the secondary structure of satellite tobacco mosaic virus and tobamovirus RNAs. Journal of General Virology 75 (1994) 2851–2856 190
Knudsen, B., Wower, J., Zwieb, C., Gorodkin, J.: tmRDB (tmRNA database). Nucleic Acids Research 29 (2001) 171–172 190
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2003 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Kim, W., Lee, Y., Han, K. (2003). Visualization of RNA Pseudoknot Structures. In: Palma, J.M.L.M., Sousa, A.A., Dongarra, J., Hernández, V. (eds) High Performance Computing for Computational Science — VECPAR 2002. VECPAR 2002. Lecture Notes in Computer Science, vol 2565. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-36569-9_12
Download citation
DOI: https://doi.org/10.1007/3-540-36569-9_12
Published:
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-00852-1
Online ISBN: 978-3-540-36569-3
eBook Packages: Springer Book Archive