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An Improved Approximation Algorithm for Scaffold Filling to Maximize the Common Adjacencies
July-Aug. 2013 (vol. 10 no. 4)
pp. 905-913
Nan Liu, Sch. of Comput. Sci. & Technol., Shandong Univ., Jinan, China
Haitao Jiang, Sch. of Comput. Sci. & Technol., Shandong Univ., Jinan, China
Daming Zhu, Sch. of Comput. Sci. & Technol., Shandong Univ., Jinan, China
Binhai Zhu, Dept. of Comput. Sci., Montana State Univ., Bozeman, MT, USA
Scaffold filling is a new combinatorial optimization problem in genome sequencing. The one-sided scaffold filling problem can be described as given an incomplete genome I and a complete (reference) genome G, fill the missing genes into I such that the number of common (string) adjacencies between the resulting genome I' and G is maximized. This problem is NP-complete for genome with duplicated genes and the best known approximation factor is 1.33, which uses a greedy strategy. In this paper, we prove a better lower bound of the optimal solution, and devise a new algorithm by exploiting the maximum matching method and a local improvement technique, which improves the approximation factor to 1.25. For genome with gene repetitions, this is the only known NP-complete problem which admits an approximation with a small constant factor (less than 1.5).
Index Terms:
optimisation,genetics,genomics,greedy strategy,optimization problem,genome sequence,one-sided scaffold filling problem,maximum matching method,NP-complete problem,common adjacencies,Bioinformatics,Genomics,Approximation methods,Approximation algorithms,Educational institutions,Algorithm design and analysis,Sequential analysis,algorithms,Comparative genomics,scaffold filling,breakpoints,adjacencies,NP-completeness
Citation:
Nan Liu, Haitao Jiang, Daming Zhu, Binhai Zhu, "An Improved Approximation Algorithm for Scaffold Filling to Maximize the Common Adjacencies," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 10, no. 4, pp. 905-913, July-Aug. 2013, doi:10.1109/TCBB.2013.100
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