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eSBH: An Accurate Constructive Heuristic Algorithm for DNA Sequencing by Hybridization

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2 Author(s)
Yang Chen ; Grad. Sch. of Inf., Production & Syst., Waseda Univ., Kitakyushu, Japan ; Jinglu Hu

Sequencing by hybridization is a promising cost-effective technology for high-throughput DNA sequencing via microarray chips. However, due to the effects of spectrum errors rooted from experimental conditions, a fast and accurate reconstruction of original sequences has become a challenging problem. In the last decade, a variety of analyses and designs have been tried to overcome this problem, where different strategies have different tradeoffs in speed and accuracy. Motivated by the idea that the errors could be identified by analyzing the interrelation of spectrum elements, this paper presents a new constructive heuristic algorithm, featuring an accurate reconstruction guided by a set of well-defined criteria and rules. The experiments on benchmark instance sets demonstrate that the proposed method can reconstruct long DNA sequences more accurately than current approaches in the literature.

Published in:

BioInformatics and BioEngineering (BIBE), 2010 IEEE International Conference on

Date of Conference:

May 31 2010-June 3 2010