Next Article in Journal
Overlays with Preferences: Distributed, Adaptive Approximation Algorithms for Matching with Preference Lists
Next Article in Special Issue
Solving Matrix Equations on Multi-Core and Many-Core Architectures
Previous Article in Journal
Stability, Optimality and Manipulation in Matching Problems with Weighted Preferences
Previous Article in Special Issue
Multi-Core Parallel Gradual Pattern Mining Based on Multi-Precision Fuzzy Orderings
Open AccessArticle

PMS6MC: A Multicore Algorithm for Motif Discovery

VMware Inc, 3401 Hillview Avenue, Palo Alto, CA 94304, USA
Department of CISE, University of Florida, Gainesville, FL 32611, USA
Department of CSE, University of Connecticut, Storrs, CT 06269, USA
Author to whom correspondence should be addressed.
Algorithms 2013, 6(4), 805-823;
Received: 15 September 2013 / Revised: 8 November 2013 / Accepted: 11 November 2013 / Published: 18 November 2013
(This article belongs to the Special Issue Algorithms for Multi Core Parallel Computation)
We develop an efficient multicore algorithm, PMS6MC, for the (l; d)-motif discovery problem in which we are to find all strings of length l that appear in every string of a given set of strings with at most d mismatches. PMS6MC is based on PMS6, which is currently the fastest single-core algorithm for motif discovery in large instances. The speedup, relative to PMS6, attained by our multicore algorithm ranges from a high of 6.62 for the (17,6) challenging instances to a low of 2.75 for the (13,4) challenging instances on an Intel 6-core system. We estimate that PMS6MC is 2 to 4 times faster than other parallel algorithms for motif search on large instances. View Full-Text
Keywords: planted motif search; parallel string algorithms; multi-core algorithms planted motif search; parallel string algorithms; multi-core algorithms
Show Figures

Figure 1

MDPI and ACS Style

Bandyopadhyay, S.; Sahni, S.; Rajasekaran, S. PMS6MC: A Multicore Algorithm for Motif Discovery. Algorithms 2013, 6, 805-823.

Show more citation formats Show less citations formats

Article Access Map

Only visits after 24 November 2015 are recorded.
Back to TopTop