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Sorting Permutations by Intergenic Operations.
IEEE/ACM Transactions on Computational Biology and Bioinformatics ( IF 4.5 ) Pub Date : 2021-05-04 , DOI: 10.1109/tcbb.2021.3077418
Andre Rodrigues Oliveira , Geraldine Jean , Guillaume Fertin , Klairton Lima Brito , Ulisses Dias , Zanoni Dias

Genome Rearrangements are events that affect large stretches of genomes during evolution. Many mathematical models have been used to estimate the evolutionary distance between two genomes based on genome rearrangements. However, most of them focused on the (order of the) genes of a genome, disregarding other important elements in it. Recently, researchers have shown that considering regions between each pair of genes, called intergenic regions, can enhance distance estimation in realistic data. Two of the most studied genome rearrangements are the reversal, which inverts a sequence of genes, and the transposition, which occurs when two adjacent gene sequences swap their positions inside the genome. In this work, we study the transposition distance between two genomes, but we also consider intergenic regions, a problem we name Sorting by Intergenic Transpositions. We show that this problem is NP-hard and propose two approximation algorithms considering two distinct definitions for the problem. We also investigate the problem called Sorting by Signed Intergenic Reversals and Intergenic Transpositions. We show that this problem is NP-hard and develop two approximation algorithms. We study how these algorithms behave when assigning weights for genome rearrangements. Finally, we implemented all these algorithms and tested them on real and simulated data.

中文翻译:

通过基因间操作对排列进行排序。

基因组重排是在进化过程中影响大范围基因组的事件。基于基因组重排,许多数学模型已用于估计两个基因组之间的进化距离。但是,他们中的大多数都将注意力集中在基因组的基因(顺序)上,而忽略了基因组中的其他重要元素。最近,研究人员表明,考虑每对基因之间的区域(称为基因间区域)可以增强现实数据中的距离估计。研究最多的两个基因组重排是反转和反转,这两个反转的反转使基因序列反转,而换位发生在两个相邻的基因序列在基因组内部交换位置时。在这项工作中,我们研究了两个基因组之间的转座距离,但同时也考虑了基因间区域,我们将这个问题称为“基因间换位排序”。我们表明该问题是NP难的,并提出了两种近似算法,考虑了该问题的两个不同定义。我们还调查了通过有符号的基因间逆转和基因间转座进行排序的问题。我们证明了这个问题是NP难的,并开发了两种近似算法。我们研究为基因组重排分配权重时这些算法的行为。最后,我们实现了所有这些算法,并在真实和模拟数据上对其进行了测试。我们证明了这个问题是NP难的,并开发了两种近似算法。我们研究为基因组重排分配权重时这些算法的行为。最后,我们实现了所有这些算法,并在真实和模拟数据上对其进行了测试。我们证明了这个问题是NP难的,并开发了两种近似算法。我们研究为基因组重排分配权重时这些算法的行为。最后,我们实现了所有这些算法,并在真实和模拟数据上对其进行了测试。
更新日期:2021-05-04
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