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.
This work was supported by grant TIN2007-66523 (FORMALISM) of the Spanish government. In addition, Christian Blum acknowledges support from the Ramón y Cajal program of the Spanish Ministry of Science and Technology of which he is a research fellow.
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Roli, A., Blum, C. (2009). Tabu Search for the Founder Sequence Reconstruction Problem: A Preliminary Study. In: Omatu, S., et al. Distributed Computing, Artificial Intelligence, Bioinformatics, Soft Computing, and Ambient Assisted Living. IWANN 2009. Lecture Notes in Computer Science, vol 5518. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-02481-8_157
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DOI: https://doi.org/10.1007/978-3-642-02481-8_157
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