Issue No. 04 - July-Aug. (2013 vol. 10)

ISSN: 1545-5963

pp: 905-913

DOI Bookmark: http://doi.ieeecomputersociety.org/10.1109/TCBB.2013.100

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

ABSTRACT

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

Bioinformatics, Genomics, Approximation methods, Approximation algorithms, Educational institutions, Algorithm design and analysis, Sequential analysis

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. , pp. 905-913, July-Aug. 2013, doi:10.1109/TCBB.2013.100CITATIONS