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Enhancing Parallel Recursive Brute Force Algorithm for Motif Finding

by Marwa A. Radad, Nawal A. El-fishawy, Hossam M. Faheem
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International Journal of Computer Applications
Foundation of Computer Science (FCS), NY, USA
Volume 86 - Number 3
Year of Publication: 2014
Authors: Marwa A. Radad, Nawal A. El-fishawy, Hossam M. Faheem
10.5120/14965-3143

Marwa A. Radad, Nawal A. El-fishawy, Hossam M. Faheem . Enhancing Parallel Recursive Brute Force Algorithm for Motif Finding. International Journal of Computer Applications. 86, 3 ( January 2014), 15-22. DOI=10.5120/14965-3143

@article{ 10.5120/14965-3143,
author = { Marwa A. Radad, Nawal A. El-fishawy, Hossam M. Faheem },
title = { Enhancing Parallel Recursive Brute Force Algorithm for Motif Finding },
journal = { International Journal of Computer Applications },
issue_date = { January 2014 },
volume = { 86 },
number = { 3 },
month = { January },
year = { 2014 },
issn = { 0975-8887 },
pages = { 15-22 },
numpages = {9},
url = { https://ijcaonline.org/archives/volume86/number3/14965-3143/ },
doi = { 10.5120/14965-3143 },
publisher = {Foundation of Computer Science (FCS), NY, USA},
address = {New York, USA}
}
%0 Journal Article
%1 2024-02-06T22:03:15.899150+05:30
%A Marwa A. Radad
%A Nawal A. El-fishawy
%A Hossam M. Faheem
%T Enhancing Parallel Recursive Brute Force Algorithm for Motif Finding
%J International Journal of Computer Applications
%@ 0975-8887
%V 86
%N 3
%P 15-22
%D 2014
%I Foundation of Computer Science (FCS), NY, USA
Abstract

Motif search is a fundamental problem in bioinformatics. Its main application is locating transcription factor binding sites (TFBSs) in DNA sequences. Numerous algorithms have been proposed in the literature to solve this problem. The exact algorithms solve M(l,d) problem by reporting all l-length motifs M with at most d mutations. Recursive Brute Force (R-BF) algorithm is an exact algorithm that has solved M(l,d) problem in exponential time with d. Multicore implementations of R-BF have efficiently utilized computation resources of modern multicore architectures to achieve more advantageous operation than sequential one. In this paper, we explore an enhanced version of R-BF algorithm. The new algorithm is called R-BF2. R-BF2 enhances the running time of R-BF by memorizing more information about each node in search space. R-BF2 pays more than 40% memory space to achieve a speedup factor of 3. However, parallel implementations of R-BF2 keep the same scalability just like R-BF on multicore systems.

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Index Terms

Computer Science
Information Sciences

Keywords

Bioinformatics Motif finding Branch & Bound search Parallel programming OpenMP MPI

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