论文信息 - On the parallel prediction of the RNA secondary structure

On the parallel prediction of the RNA secondary structure

Publisher Summary This chapter discusses the parallelization of the Vienna package algorithm that predicts the secondary structure of the RNA. Before the tool can be effectively used, it must be tuned on the target architecture. This tune consists of finding the tile sizes for optimal executions. The analytical model is developed to find these optimal tile sizes. The validity of the analytical model developed for the parallel algorithms presented is studied through an extensive set of experiments performed on a Origin 3000. A statistical model is presented, to deal with the cases where the hypothesis of the analytical model is not satisfied. The algorithms are satisfactorily applied to real sequences. The algorithm is applied to real sequences. The speedups, although satisfactory, do not scale for some of those instances— that is, p 3 8. This is probably due to the use of a common static tile size. A dynamic variable tile size on every macro-rectangle is introduced in the chapter.

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