Development of MapReduce and MPI Programs for Motif Search
Document Type
Conference Proceeding
Publication Date
10-26-2015
Abstract
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.
DOI
10.1109/CLUSTER.2015.82
Montclair State University Digital Commons Citation
Safran, Mejdl; Al-Qahtani, Saad; Zhu, Michelle; and Che, Dunren, "Development of MapReduce and MPI Programs for Motif Search" (2015). Department of Computer Science Faculty Scholarship and Creative Works. 219.
https://digitalcommons.montclair.edu/compusci-facpubs/219