CPDP: A Connection based PDP Algorithm

Partial Digest Problem (PDP) is a critical problem of computational biology that deals with the point set realization of a pair-wise distance multiset. The points in the set correspond to a collection of restriction sites that reflects the points of cleaves of a DNA sequence on addition of a restriction enzyme into a DNA solution. The PDP problem bears analogy to the “turnpike reconstruction problem” of computer science where the points dwell on a line and the “beltway problem” where the points reside on a loop. Although the partial digest problem has numerous applications in genetics, yet it is computationally hard to solve. In fact the NP-complete nature of PDP for random dataset and the NP-hard nature for Zhang instances have attracted numerous researchers to trim its execution time. Several approaches ranging from pseudo-polynomial time algorithms to genetic algorithms and backtracking algorithms have been suggested for PDP. This paper presents an algorithm which reduces the search space significantly for the application of backtracking. The connection based PDP algorithm (CPDP) proposed here gives exact results when run for random as well as hard instances of data as defined by Zhang.