Optimization of an RNA Folding Algorithm for Parallel Architectures

  title={Optimization of an RNA Folding Algorithm for Parallel Architectures},
  author={Jih-Hsiang Chen and Shu-Yun Le and Bruce A. Shapiro and Jacob V. Maizel},
  journal={Parallel Computing},
In this paper we describe parallel implementations of a dynamic programming algorithm for predicting ribonucleic acid (RNA) secondary structure based on energy minimization in high performance computers. The computations of the energies for all possible fragments of the molecule consume almost all the computations in the prediction algorithm. The computation ordering and the data placement dictate the performance of the algorithm. Only the diagonal ordering, which starts with short fragments… CONTINUE READING
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