NDLI: Scalable Multi-core Implementation for Motif Finding Problem

Content Provider	IEEE Xplore Digital Library
Author	Abbas, M.M. Malluhi, Q.M. Balakrishnan, P.
Copyright Year	2014
Description	Author affiliation: KINDI Lab. for Comput. Res., Qatar Univ., Doha, Qatar (Abbas, M.M.; Malluhi, Q.M.; Balakrishnan, P.)
Abstract	The motif finding problem is a key step for understanding the gene regulation and expression, drug design, disease resistance, etc. Many sequential algorithms have been proposed in the literature to find the exact motifs. Voting algorithm is one such memory and time efficient sequential solution for motif finding. In this paper, we develop a parallel version of CVoting algorithm realized using openMP. The paper evaluates this parallel algorithm on a multi-core architecture using both simulated and real datasets. The paper compares the performance against existing multi-core implementations. Our experiments show that, the scalability of our implementation is linear for all challenging instances running on different number of processors, while the scalability of other implementations varies with respect to motif length or the number of processors. The average efficiency of our parallel implementations for all instances is more than 90%.
Starting Page	178
Ending Page	183
File Size	809435
Page Count	6
File Format	PDF
ISBN	9781479959181
e-ISBN	9781479959198
DOI	10.1109/ISPDC.2014.27
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2014-06-24
Publisher Place	France
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Program processors Scalability Algorithm design and analysis Approximation algorithms DNA Approximation methods Prediction algorithms Voting algorithm motif finding multi-core challenging instances
Content Type	Text
Resource Type	Article

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3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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