Visualization of RNA Pseudoknot Structures
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.
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