DNA Directed Model for Shortest Superstring Problem

DNA is increasingly being used as the engineering material of choice for the construction of nanoscale circuits, structures, and motors. Recent experimental and theoretical advances have produced and tested new methods to obtain large DNA word sets to support virtually any kind of applications. The problem of finding a Shortest Common Supersequence (SCS) of a set of sequences is an important problem with applications in many areas. This problem is NP-hard and has applications in computational biology and data compression. In this paper, we present a graph model of SCS problem. We characterize the shortest superstring as a Hamiltonian path in a directed graph and give a algotirhm for solving large SCS instances of biological sequences in linear time. As a general computational framework, this algorithm can also be applied on more general applications such as text comparison and compression, query optimization and scheduling.