A randomized iterated greedy algorithm for the founder sequence reconstruction problem
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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. Basing our work on previous ideas outlined in , we developed a randomized iterated greedy algorithm that is able to provide good solutions in a short time span. The experimental evaluation shows that our algorithm is currently the best approximate technique, especially when large problem instances are concerned.
CitacióBenedettini, S.; Blum, C.; Roli, A. A randomized iterated greedy algorithm for the founder sequence reconstruction problem. "Lecture notes in computer science", Abril 2010, núm. 6073, p. 37-51.
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