A New Approximation Algorithm for Genomic Scaffold Filling Based on Contig

Genomic scaffold filling problem is an important combinatorial optimization problem belonging to computational genomics. The One-Sided Genomic Scaffold Filling problem based on contig (One-Sided-SF-max) is the focus in this paper. The scaffold in this problem is presented as a sequence of contigs. The missing genes only can be inserted between contigs to ensure the integrity of original contigs. In this paper, an improved algorithm with a factor of
$\frac{15}{8}$
is proposed using the maximum matching and greedy method. The goal is to maximize the number of common adjacencies between two sequences. The approximate ratio of the algorithm is proved. Compared with the 2-approximation algorithm, the execution efficiency of the algorithm is also improved by running the same simulated data in the experiments of the two algorithms.