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PLEACH: a new heuristic algorithm for pure parsimony haplotyping problem

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Abstract

Haplotype inference is an important issue in computational biology due to its various applications in diagnosing and treating genetic diseases such as diabetes, Alzheimer, and heart defects. There are different criteria to choose the solution from the alternatives. Parsimony is one of the most important criteria according to which the problem is known as Pure Parsimony Haplotyping (PPH) problem. The approaches to solve PPH are classified to two groups: exact and non-exact. The exact approaches often model the problem as a Mixed Integer Linear Programming (MILP) problem. Although in solving the small instances, these models generate the optimal solution in a reasonable time, because of the NP-hardness characteristic of PPH problem, they are ineffective in solving very large instances. This deficiency is compensated by non-exact algorithms. In this paper, we present a non-exact algorithm for large instances of PPH problem based on the divide-and-conquer technique. This algorithm, first, divides the problem into small sub-problems, which are solved by one of the previous exact approaches, and finally the solutions of the sub-problems are combined through solving an MILP. The appeared MILPs for solving the sub-problems and those for combining the solutions are so small that are solved rapidly. The performance of this algorithm has been evaluated by implementing it on real and simulated instances and in comparison with two well-known methods of PHASE and WinHap2.

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Acknowledgements

The authors are grateful to the anonymous reviewers for their helpful comments which lead to this improved version of the paper.

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Authors and Affiliations

  1. Department of Applied Mathematics, Faculty of Mathematical Science, University of Guilan, Rasht, Iran

    Reza Feizabadi, Mehri Bagherian & Maziar Salahi

  2. Department of Biology, Faculty of Science, University of Guilan, Rasht, Iran

    Hamidreza Vaziri

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  1. Reza Feizabadi
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  4. Maziar Salahi
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All authors were involved in proposing and writing the paper. R. Feizabadi conducted the implementations of codes.

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Correspondence to Mehri Bagherian.

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Feizabadi, R., Bagherian, M., Vaziri, H. et al. PLEACH: a new heuristic algorithm for pure parsimony haplotyping problem. J Supercomput 80, 8236–8258 (2024). https://doi.org/10.1007/s11227-023-05746-7

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