Visualization method of RNA pseudoknot structures

Details Visualization method of RNA pseudoknot structures Visualization method of RNA pseudoknot structures

2006-11-14

2006-11-14

Zeman, Mark K. (Department: 1631)

Data processing: measuring, calibrating, or testing

Measurement system in a specific environment

Biological or biochemical

C702S019000, C703S011000, C435S006120, C707S793000

Reexamination Certificate

active

07136760

ABSTRACT:
Disclosed is a visualization method of RNA pseudoknot structures. The method of the invention comprises the steps of setting criteria required for visualizing RNA pseudoknots, setting structural elements and data structures for representing a whole RNA structure containing pseudoknots, determining an input format for visualization and a drawing order of the structure, determining connectivity relations between regular loops and stems in the structure and between pseudoknot loops and stems in the structure, calculating radii of the regular loop and the PK loop, calculating coordinates of bases in the regular loops, setting internal angles of the PK loops, calculating startAngles of the regular loops and angles of the stem, determining positions of the pseudoknots in the PK loops, and drawing the pseudoknots and the whole RNA structure containing the pseudoknots.

REFERENCES:
‘A vector-based method for drawing RNA secondary structurez’, by Kyungsook Han, Dohyung Kim and Hong-lim Kim, Bioinformatics, vol. 15, No. 4, pp. 286-297 (1999).
Rnaviz, a program for the visualization of RNA secondary structure, by Peter De Rijk and Rupert De Wachter, Nucelic Acids Research, vol. 25, No. 22, pp. 4679-4684 (1997).
New Developments in Structure Determination of Pseudoknots, Cornelis W. Hilbers, Paul J.A. Michiels, Hans A. Heus, Biopolymers (Nucleic Acid Sciences), vol. 48, pp. 137-153 (1998).
PseudoBase: structuraz information on RNA pseudoknotst, F.H.D. van Batenburg, A.P. Gutyaev and C.W.A. Pleij, Nucleic Acids Research, vol. 29, No. 1, pp. 194-195 (2001).
“Pseudoviewer”, available at http://pseudoviewer.inha.ac.kr as provided by a web intelligence laboratory at Inha University, 253 Younghyun-dong, Nam-gu lncheon, 402-751.

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