Tabu search for the founder sequence reconstruction problem: a preliminary study

Abstract

The problem of inferring ancestral genetic information in terms of a set of founders of a given population arises in various biological contexts. In optimization terms, this problem can be formulated as a combinatorial string problem. The main problem of existing techniques, both exact and heuristic, is that their time complexity scales exponentially, which makes them impractical for solving large-scale instances. We developed a new constructive heuristic and a tabu search method with the explicit aim of providing solutions in a reduced amount of computation time. Experimental results show that when the number of founders grows, our algorithms have advantages over the ones proposed in the literature.