VISUALIZATION OF RNA SECONDARY STRUCTURES USING HIGHLY PARALLEL COMPUTERS

Results of RNA secondary structure prediction algorithm are usually gi ven as a set of hydrogen bonds between bases. However, we cannot know the precise structure of an RNA molecule by only knowing which bases f orm hydrogen bonds. One way to understand the structure of an RNA mole cule is to visualize it using a planar graph so that we can easily kno w the geometric relations among the substructures such as stacking reg ions and loops. To do this, we consider bases to be particles on a pla ne and introduce a repulsive force and an attractive force among these particles and determine their positions according to these forces. A naive algorithm requires O(N-2) time but we can reduce it to O(NlogN) with an approximation algorithm which is often used in the al ea of N- body simulation. Our program is written in parallel object-oriented la nguage 'Schematic' which is recently developed. Efficiency of our impl ementation on a parallel computer and results of visualization of seco ndary structures are presented using cadang-cadang coconut viroid as a n example.