Abstract

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.