Accurate reconstruction for DNA sequencing by hybridization based on a constructive heuristic

Yang Chen*, Jinglu Hu


研究成果: Article査読

3 被引用数 (Scopus)


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.

ジャーナルIEEE/ACM Transactions on Computational Biology and Bioinformatics
出版ステータスPublished - 2011

ASJC Scopus subject areas

  • バイオテクノロジー
  • 遺伝学
  • 応用数学


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