Abstract
Visualization of a complex molecular structure is a valuable tool in understanding the structure. A drawing of RNA pseudoknot structures is a graph (and a possibly nonplanar graph) with inner cycles within a pseudoknot as well as possible outer cycles formed between a pseudoknot and other structural elements. Thus, drawing RNA pseudoknot structures is computationally more difficult than depicting RNA secondary structures. Although several algorithms have been developed for drawing RNA secondary structures, none of these can be used to draw RNA pseudoknots and thus visualizing RNA pseudoknots relies on significant amount of manual work. Visualizing RNA pseudoknots by manual work becomes more difficult and yields worse results as the size and complexity of the RNA structures increase. We have developed a new representation method and an algorithm for visualizing RNA pseudoknots as a twodimensional drawing and implemented the algorithm in a program. The new representation produces uniform and clear drawings with no edge crossing for all kinds of pseudoknots, including H-type and other complex types. Given RNA structure data, we represent the whole structure as a tree rather than as a graph by hiding the inner cycles as well as the outer cycles in the nodes of the abstract tree. Once the top-level RNA structure is represented as a tree, nodes of the tree are placed and drawn in increasing order of their depth values. Experimental results demonstrate that the algorithm generates a clear and aesthetically pleasing drawing of large-scale RNA structures, containing any number of pseudoknots. This is the first algorithm for automatically drawing RNA structure with pseudoknots.
Keywords
- Isosceles Triangle
- Hairpin Loop
- Circle Shape
- Complex Molecular Structure
- Outer Cycle
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.
Research supported by the Korea Science and Engineering Foundation (KOSEF) under grant R05-2001-000-01037-0.
This is a preview of subscription content, access via your institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsPreview
Unable to display preview. Download preview PDF.
References
De Rijk, P., De Wachter, R.: RnaVIz, a program for the visualization of RNA secondary structure. Nucleic Acids Res. 25 (1997) 4679–4684
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 Res. 25 (1997) 1130–1135
Gultyaev, A.P., van Batenburg, E., Pleij, C.W.A.: Similarities between the secondary structure of satellite tobacco mosaic virus and tobamovirus RNAs. J. Gen. Virology 75 (1994), 2851–2856
Han, K., Kim, D., Kim, H.-J.: A vector-based method for drawing RNA secondary structure. Bioinformatics 15 (1999) 286–197
Hilbers, C.W., Michiels, P.J.A., Heus, H.A.: New Developments in Structure Determination of Pseudoknots. Biopolymers 48 (1998) 137–153
Pleij, C.W.A.: Pseudoknots: a new motif in the RNA game. Trends in Biochemical Sciences 15 (1990) 143–147
van Batenburg, F.H.D., Gultyaev, A.P., Pleij, C.W.A.: PseudoBase: structural information on RNA pseudoknots. Nucleic Acids Res. 29 (2001) 194–195
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2002 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Lee, Y., Kim, W., Han, K. (2002). New Representation and Algorithm for Drawing RNA Structure with Pseudoknots* . In: Kambayashi, Y., Winiwarter, W., Arikawa, M. (eds) Data Warehousing and Knowledge Discovery. DaWaK 2002. Lecture Notes in Computer Science, vol 2454. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-46145-0_19
Download citation
DOI: https://doi.org/10.1007/3-540-46145-0_19
Published:
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-44123-6
Online ISBN: 978-3-540-46145-6
eBook Packages: Springer Book Archive