Parallel implementation of quorum planted (ℓ, d) motif search on multi-core/many-core platforms

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 imple...

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Bibliographic Details
Published in:Microprocessors and microsystems 2016-10, Vol.46, p.255-263
Main Authors: Kazemian, Fazeleh Sadat, Fazlali, Mahmood, Katanforoush, Ali, Rezvani, Mojtaba
Format: Article
Language:English
Subjects:
Algorithm decomposition
Motif finding
Thread parallelization
Thread scheduling
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Summary: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.
ISSN:0141-9331
1872-9436
DOI:10.1016/j.micpro.2016.06.008