A vector-based method for drawing RNA secondary structure

MOTIVATION To produce a polygonal display of RNA secondary structure with minimal overlap and distortion of structural elements, with minimal search for positioning them, and with minimal user intervention. RESULTS A new algorithm for automatically drawing RNA secondary structure has been developed. The algorithm represents the direction and space for a structural element using vector and vector space. Two heuristics are used. The first heuristic is concerned with ordering structural elements to be positioned and the second with positioning them in space. The algorithm and a graphical user interface have been implemented in a working program called VizQFolder on IBM PC compatibles. Experimental results demonstrate that VizQFolder is capable of automatically generating nearly overlap-free polygonal displays for long RNA molecules. The only distortion performed to avoid overlap is the rotation of helices, leading to efficient generation of a polygonal display without sacrificing its readability. VizQFolder is not coupled to a specific prediction program of RNA secondary structure, and thus can be used for visualizing secondary structure models obtained by any means. AVAILABILITY The executable code of VizQFolder is available at http://automation.inha.ac.kr/khan. It can also be obtained from the authors upon request.