Abstract
Conference Title: 2015 IEEE International Conference on Cluster Computing (CLUSTER) Conference Start Date: 2015, Sept. 8 Conference End Date: 2015, Sept. 11 Conference Location: Chicago, IL, USA As one of the important problems in molecular biology, motif search is computationally expensive, especially when the size of DNA sequences is large. Extended from a graduate course project in parallel and distributed computing (PDC), this paper investigates two different programming frameworks, namely MapReduce and MPI on motif finding. We implemented a serial algorithm, a MapReduce based algorithm, and a MPI program to calculate the best motif in given DNA sequences. The experimental results demonstrate that our MPI program outperformed both the MapReduce-based algorithm and the serial program with superior efficiency.