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Heuristics for the Reversal and Transposition Distance Problem.
IEEE/ACM Transactions on Computational Biology and Bioinformatics ( IF 4.5 ) Pub Date : 2019-10-07 , DOI: 10.1109/tcbb.2019.2945759
Klairton Lima Brito , Andre Rodrigues Oliveira , Ulisses Dias , Zanoni Dias

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.

中文翻译:

逆向和换位距离问题的启发式方法。

我们提出了三种启发式方法:“滑动窗口”,“向前看”和“迭代滑动窗口”,以改进“通过逆转和换位问题对有符号排列进行排序”的解决方案。我们研究问题的经典版本以及仅限于前缀和前缀或后缀操作的版本。为了评估基于启发式算法的改进,我们实施了文献中描述的算法以提供初始解决方案。尽管我们遇到的问题数量有限,但是这些启发式方法可以应用于基因组重排领域中的许多其他问题。如果时间是关键因素,则“滑动窗口”是线性时间,因此是更好的选择。如果解决方案的质量是重中之重,则应优先考虑。
更新日期:2020-03-07
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