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Advances in Bioinformatics
Volume 2013 (2013), Article ID 793130, 6 pages
http://dx.doi.org/10.1155/2013/793130
Research Article

Efficient Serial and Parallel Algorithms for Selection of Unique Oligos in EST Databases

1Department of Computer Science, Memorial University, Canada
2Department of Mathematics and Statistics, Memorial University, Canada

Received 15 October 2012; Accepted 14 February 2013

Academic Editor: Alexander Zelikovsky

Copyright © 2013 Manrique Mata-Montero et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

Obtaining unique oligos from an EST database is a problem of great importance in bioinformatics, particularly in the discovery of new genes and the mapping of the human genome. Many algorithms have been developed to find unique oligos, many of which are much less time consuming than the traditional brute force approach. An algorithm was presented by Zheng et al. (2004) which finds the solution of the unique oligos search problem efficiently. We implement this algorithm as well as several new algorithms based on some theorems included in this paper. We demonstrate how, with these new algorithms, we can obtain unique oligos much faster than with previous ones. We parallelize these new algorithms to further improve the time of finding unique oligos. All algorithms are run on ESTs obtained from a Barley EST database.