eSBH: An accurate constructive heuristic algorithm for DNA sequencing by hybridization

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Citation (Scopus)

Abstract

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.

Original languageEnglish
Title of host publication10th IEEE International Conference on Bioinformatics and Bioengineering 2010, BIBE 2010
Pages124-129
Number of pages6
DOIs
Publication statusPublished - 2010
Event10th IEEE International Conference on Bioinformatics and Bioengineering, BIBE-2010 - Philadelphia, PA
Duration: 2010 May 312010 Jun 3

Other

Other10th IEEE International Conference on Bioinformatics and Bioengineering, BIBE-2010
CityPhiladelphia, PA
Period10/5/3110/6/3

Fingerprint

Benchmarking
High-Throughput Nucleotide Sequencing
Heuristic algorithms
DNA Sequence Analysis
DNA
Technology
Costs and Cost Analysis
DNA sequences
Microarrays
Throughput
Costs
Experiments
Heuristics

ASJC Scopus subject areas

  • Biomedical Engineering
  • Health Informatics

Cite this

Chen, Y., & Furuzuki, T. (2010). eSBH: An accurate constructive heuristic algorithm for DNA sequencing by hybridization. In 10th IEEE International Conference on Bioinformatics and Bioengineering 2010, BIBE 2010 (pp. 124-129). [5521701] https://doi.org/10.1109/BIBE.2010.29

eSBH : An accurate constructive heuristic algorithm for DNA sequencing by hybridization. / Chen, Yang; Furuzuki, Takayuki.

10th IEEE International Conference on Bioinformatics and Bioengineering 2010, BIBE 2010. 2010. p. 124-129 5521701.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Chen, Y & Furuzuki, T 2010, eSBH: An accurate constructive heuristic algorithm for DNA sequencing by hybridization. in 10th IEEE International Conference on Bioinformatics and Bioengineering 2010, BIBE 2010., 5521701, pp. 124-129, 10th IEEE International Conference on Bioinformatics and Bioengineering, BIBE-2010, Philadelphia, PA, 10/5/31. https://doi.org/10.1109/BIBE.2010.29
Chen Y, Furuzuki T. eSBH: An accurate constructive heuristic algorithm for DNA sequencing by hybridization. In 10th IEEE International Conference on Bioinformatics and Bioengineering 2010, BIBE 2010. 2010. p. 124-129. 5521701 https://doi.org/10.1109/BIBE.2010.29
Chen, Yang ; Furuzuki, Takayuki. / eSBH : An accurate constructive heuristic algorithm for DNA sequencing by hybridization. 10th IEEE International Conference on Bioinformatics and Bioengineering 2010, BIBE 2010. 2010. pp. 124-129
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