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Heuristics for the Reversal and Transposition Distance Problem.

08:00 EDT 7th October 2019 | BioPortfolio

Summary of "Heuristics for the Reversal and Transposition Distance Problem."

We present three heuristics - Sliding Window, Look Ahead, and Iterative Sliding Window - to improve solutions for the Sorting Signed Permutations by Reversals and Transpositions Problem. We investigate the classical version of the problem as well as versions restricted to prefix and prefix or suffix operations. To assess the heuristics based on its improvement, we implemented algorithms described in the literature to provide initial solutions. Although we have a limited number of problems, these heuristics can be applied to many others within the area of genome rearrangement. When time is a crucial factor, Sliding Window is a better choice because it runs in linear time. If the quality of the solution is a priority, Look Ahead should be preferred. Iterative Sliding Window is the most flexible heuristic and allows us to find a trade-off for specific scenarios where running time and solution quality are relevant.

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This article was published in the following journal.

Name: IEEE/ACM transactions on computational biology and bioinformatics
ISSN: 1557-9964
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