The algorithm for the two-sided scaffold filling problem

Abstract

Scaffold filling is a new combinatorial optimization problem in genome sequencing and can improve the accuracy of the sequencing results. The two-sided Scaffold Filling to Maximize the Number of String Adjacencies(SF-MNSA) problem can be described as: given two incomplete gene sequences A and B, respectively fill the missing genes into A and B such that the number of adjacencies between the resulting sequences A′ and B′ is maximized. The two-sided scaffold filling problem is NP-complete for genomes with duplicated genes and there is no effective approximation algorithm. In this paper, we propose a new version problem that symbol # is added to each end of each input sequence for any instance of two-sided SF-MNSA problem and design a polynomial algorithm for one special case of this new version problem. For any instance, we present a better lower bound of the optimal solution and devise a factor-1.5 approximation algorithm by exploiting greedy strategy. © Springer-Verlag Berlin Heidelberg 2013.