Speeding Up the Partial Digest Algorithm

Abstract

We consider the partial digest problem, which aims to find the setIn bioinformatics, the lengths of DNA fragments represents the multiset D, while the set of restriction site locations represents the set X = {x 0 , x 1 , . . . , x n }. In this paper, we study experimentally the effect of increasing and decreasing the number of levels on the breadth-breadth algorithm which is the best practical algorithm for the partial digest problem. The experimental study shows that the running time of breadth-breadth method is not the minimum time. Also, we obtained the number of levels that is used in the breadth-breadth algorithm to reduce the running time.