Visualization of RNA Pseudoknot Structures

초록

RNA pseudoknots are not only important structural elements for forming the tertiary structure, but also responsible for several functions of RNA molecules such as frameshifting, 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 RNA pseudoknot 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. The algorithm has been implemented in a Java program, which can be executed on any computing systems. Experimental results show that this program generates a clear and compact drawing of RNA pseudoknots and allows a biologist to gain insights into RNA pseudoknot structures. The program can also be used as useful aids in designing biochemical experiments to elucidate more precise mechanism of RNA functions associated with pseudoknots.