The most common way to calculate the rearrangement distance between two genomes is to use the size of a minimum length sequence of rearrangements that transforms one of the two given genomes into the other, where the genomes are represented as permutations using only their gene order, based on the assumption that genomes have the same gene content. With the advance of research in genome rearrangements, new works extended the classical models by either considering genomes with different gene content (unbalanced genomes) or including more genomic characteristics to the mathematical representation of the genomes, such as the distribution of intergenic regions sizes. In this study, we study the Reversal, Transposition, and Indel (Insertion and Deletion) Distance using intergenic information, which allows comparing unbalanced genomes, because indels are included in the rearrangement model (i.e., the set of possible rearrangements allowed when we compute the distance). For the particular case of transpositions and indels on unbalanced genomes, we present a 4-approximation algorithm, improving a previous 4.5 approximation. This algorithm is extended so as to deal with gene orientation and to maintain the 4-approximation factor for the Reversal, Transposition, and Indel Distance on unbalanced genomes. Furthermore, we evaluate the proposed algorithms using experiments on simulated data.

中文翻译：

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使用基因间信息对不平衡基因组进行逆转和转座距离。

计算两个基因组之间重排距离的最常见方法是使用重排的最小长度序列的大小，该重排序列将两个给定基因组之一转换为另一个基因组，其中基因组仅使用其基因顺序表示为排列，基于假设基因组具有相同的基因内容。随着基因组重排研究的进步，新的工作通过考虑具有不同基因内容的基因组（不平衡基因组）或在基因组的数学表示中包含更多基因组特征（例如基因间区域大小的分布）来扩展经典模型。在本研究中，我们使用基因间信息研究反转、转座和插入缺失（插入和删除）距离，这允许比较不平衡的基因组，因为插入缺失包含在重排模型中（即，当我们计算距离）。对于不平衡基因组上的转座和插入缺失的特殊情况，我们提出了一种 4 近似算法，改进了之前的 4.5 近似。该算法被扩展以处理基因方向并维持不平衡基因组上反转、转置和插入缺失距离的 4 近似因子。此外，我们使用模拟数据实验来评估所提出的算法。