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Accurate Reconstruction for DNA Sequencing by Hybridization Based on a Constructive Heuristic
July/August 2011 (vol. 8 no. 4)
pp. 1134-1140
Yang Chen, Waseda University, Fukuoka
Jinglu Hu, Waseda University, Fukuoka
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 in experimental conditions, an accurate and fast 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 trade-offs 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 constructive heuristic algorithm, featuring an accurate reconstruction guided by a set of well-defined criteria and rules. Instead of directly reconstructing the original sequence, the new algorithm first builds several accurate short fragments, which are then carefully assembled into a whole sequence. The experiments on benchmark instance sets demonstrate that the proposed method can reconstruct long DNA sequences with higher accuracy than current approaches in the literature.

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Index Terms:
DNA sequencing, sequencing by hybridization, heuristic algorithm, bioinformatics, microarrays.
Citation:
Yang Chen, Jinglu Hu, "Accurate Reconstruction for DNA Sequencing by Hybridization Based on a Constructive Heuristic," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 8, no. 4, pp. 1134-1140, July-Aug. 2011, doi:10.1109/TCBB.2010.89
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