Assembling DNA fragments with parallel algorithms

As more research centers embark on sequencing new genomes, the problem of DNA fragment assembly for shotgun sequencing is growing in importance and complexity. Accurate and fast assembly is a crucial part of any sequencing project and since the DNA fragment assembly problem is NP-hard, exact solutions are very difficult to obtain. Various heuristics, including genetic algorithms, were designed for solving the fragment assembly problem. While the sequential genetic algorithm has given good results, it is unable to sequence very large DNA molecules. In this work, we present two parallel methods, a distributed genetic algorithm and a parallel simulated annealing, to solve problem instances that are 77K base pairs long accurately