Title: A parallel combinatorial algorithm for subtle motifs

Authors: Michael Arock, Srinivasulu Reddy, A.V. Reddy

Addresses: Department of Computer Applications, National Institute of Technology, Tiruchirappalli 620 015, Tamil Nadu, India. ' Department of Computer Applications, National Institute of Technology, Tiruchirappalli 620 015, Tamil Nadu, India. ' Department of Computer Applications, National Institute of Technology, Tiruchirappalli 620 015, Tamil Nadu, India

Abstract: In bioinformatics, motif finding is one of the most common problems. It is to locate recurring patterns in the sequence of nucleotides or amino acids. The main difficulty of the problem is that the patterns are not exact matches owing to biological mutations. It is NP-complete. Within the literature many solutions have been provided for this challenging problem. Nevertheless, they do not address certain subtleties. Among them, one is addressed by Hu (2003). In this paper, we propose a parallel combinatorial algorithm for subtle motif finding on a Shared Memory Multiprocessor model. We suggest a method of implementation for the same.

Keywords: motif finding; subtle motifs; combinatorics; parallel algorithms; EREW PRAM model; DSM; distributed shared memory; bioinformatics; recurring patterns; sequences; nucleotides; amino acids; shared memory multiprocessor.

DOI: 10.1504/IJBRA.2010.034074

International Journal of Bioinformatics Research and Applications, 2010 Vol.6 No.3, pp.260 - 269

Received: 17 Nov 2007
Accepted: 03 Nov 2008
Published online: 07 Jul 2010 *

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