Development of MapReduce and MPI Programs for Motif Search
Safran, Mejdl . 2015
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.
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