An improved approximation algorithm for scaffold filling to maximize the common adjacencies

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. © 2013 Springer-Verlag Berlin Heidelberg.