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Multiprocessor implementation of modeling method for Planted Motif Problem

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2 Author(s)
Subrahmanyam Desaraju ; Department of Computer Science, Old Dominion University, Norfolk, VA, USA ; Ravi Mukkamala

The Planted Motif Problem is a pattern-finding problem that arises in computational biology. In our previous work, we used Modeling Method has to solve these problems up to a size of (48, 12). For a certain range of problem sizes, the Modeling Method is much faster than other methods described in the literature. However, outside this range, the method is very slow, and this imposes a practical limitation on the range of problem sizes that can be solved by it. Here, we describe a multiprocessor implementation of the Modeling Method, which increases the range of problem sizes that can be solved in practical times. We also present a comprehensive table of running times observed to be taken by the multiprocessor implementation, to solve 52 problems over a range of problem sizes.

Published in:

Information and Communication Technologies (WICT), 2011 World Congress on

Date of Conference:

11-14 Dec. 2011