Visualization method of RNA pseudoknot structures

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

2011-07-05

2011-07-05

Sims, Jason (Department: 1631)

Data processing: measuring, calibrating, or testing

Measurement system in a specific environment

Biological or biochemical

C703S002000

Reexamination Certificate

active

07974786

ABSTRACT:
The present invention relates to a visualization method of RNA pseudoknot structures for more efficiently and clearly visualizing all types of RNA pseudoknot structures including H-types in the form of a planar graph without edge-crossing so that the structures can be easily examined. The visualization method comprises reading the structure data in bracket view, identifying stem-loops and pseudoknots enclosed in bracket pairs from the input structure data, first computing the position and shape of a stem-loop contained in an identified pseudoknot to visualize the stem-loop, second computing the position and shape of the pseudoknot containing the calculated stem-loop to visualize the pseudoknot, third computing the position and shape of a stem-loop outside the computed pseudoknot, and inserting or connecting the visualized stem-loops into or to the pseudoknots to complete an RNA pseudoknot structure drawing.

REFERENCES:
patent: 7136760 (2006-11-01), Han et al.
Lee et al., New Representation and Algorithm for Drawing RNA Structure with Pseudoknots, Springerlinked Jan. 1, 2002, Springer-Verlag Berlin Heidelberg, pp. 191-201.

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