TY - JOUR
T1 - Parallel implementation of quorum planted (ℓ, d) motif search on multi-core/many-core platforms
AU - Kazemian, Fazeleh Sadat
AU - Fazlali, Mahmood
AU - Katanforoush, Ali
AU - Rezvani, Mojtaba
N1 - Publisher Copyright:
© 2016 Elsevier B.V.
PY - 2016/10/1
Y1 - 2016/10/1
N2 - Multi-core and many-core architectures are widely adopted by researchers in applied sciences and engineering, owing to their reasonable cost, and ease of access. Moreover, their painless hardware set-up process and rather simple programming paradigm attract more researchers to acquire them and implement their time-expensive computations on these platforms. Planted Motif Search problem is one of the most challenging problems in bioinformatics whose goal is to enumerate all strings of length ℓ that are commonly planted in a given set of DNA sequences. In this paper, we propose an efficient method of thread parallelization to accelerate the latest Quorum Planted Motif Search algorithm (qPMS9) on multi-core and many-core systems. Our contribution towards dynamic scheduling of threads and parallelization of loops in the proposed method outperforms previous sequential and parallel algorithms.
AB - Multi-core and many-core architectures are widely adopted by researchers in applied sciences and engineering, owing to their reasonable cost, and ease of access. Moreover, their painless hardware set-up process and rather simple programming paradigm attract more researchers to acquire them and implement their time-expensive computations on these platforms. Planted Motif Search problem is one of the most challenging problems in bioinformatics whose goal is to enumerate all strings of length ℓ that are commonly planted in a given set of DNA sequences. In this paper, we propose an efficient method of thread parallelization to accelerate the latest Quorum Planted Motif Search algorithm (qPMS9) on multi-core and many-core systems. Our contribution towards dynamic scheduling of threads and parallelization of loops in the proposed method outperforms previous sequential and parallel algorithms.
KW - Algorithm decomposition
KW - Motif finding
KW - Thread parallelization
KW - Thread scheduling
UR - http://www.scopus.com/inward/record.url?scp=84995687636&partnerID=8YFLogxK
U2 - 10.1016/j.micpro.2016.06.008
DO - 10.1016/j.micpro.2016.06.008
M3 - Article
SN - 0141-9331
VL - 46
SP - 255
EP - 263
JO - Microprocessors and Microsystems
JF - Microprocessors and Microsystems
ER -