Rearrangement is one of the most studied features in the animal mitochondrial genomes. The progress in high-throughput sequencing and comparative genomics has brought opportunities for systematic studies of mitochondrial genome rearrangements. However, there are few reports on globally examining mitogenome rearrangement and distinguishing the rearrangement frequency of each gene, which could contribute to a better understanding of its models and evolution. We presented qMGR, a new approach for large-scale quantifying mitogenome rearrangements considering a single gene as a structural unit. Compared to a reference arrangement, qMGR accumulates the changes of two nearest neighbor genes to calculate rearrangement score (RS) and rearrangement frequency (RF) of each single gene in the mitogenomes of a given taxonomic group. By accumulating RS of all genes in one genome, qMGR was developed to calculate each mitogenome rearrangement score, which can be used as a quantitative feature of the mitogenome rearrangement. Based on the frequency of rearrangement of each gene, qMGR can further detect the conserved gene set and high frequency rearrangement segments within the taxon. They may facilitate the assessment of rearrangement distances and understanding rearrangement mechanisms. qMGR web service is freely available at http://qmgr.hnnu.edu.cn/. The source code is available under GNU GPL at https://github.com/zhanglab2019/qMGR.

中文翻译：

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qMGR：量化线粒体基因组重排的新方法

重排是动物线粒体基因组中研究最多的特征之一。高通量测序和比较基因组学的进步为线粒体基因组重排的系统研究带来了机会。然而，很少有关于全局检查有丝分裂基因组重排和区分每个基因的重排频率的报道，这有助于更好地理解其模型和进化。我们提出了 qMGR，这是一种将单个基因作为结构单元的大规模量化有丝分裂基因重排的新方法。与参考排列相比，qMGR 累积了两个最近邻基因的变化，以计算给定分类组的有丝分裂基因组中每个单个基因的重排评分 (RS) 和重排频率 (RF)。通过累积一个基因组中所有基因的 RS，开发了 qMGR 来计算每个有丝分裂基因组重排评分，该评分可作为有丝分裂基因组重排的定量特征。基于每个基因的重排频率，qMGR 可以进一步检测分类单元内的保守基因集和高频重排片段。它们可能有助于评估重排距离和理解重排机制。qMGR 网络服务可在 http://qmgr.hnnu.edu.cn/ 免费获得。源代码可在 GNU GPL 下获得，网址为 https://github.com/zhanglab2019/qMGR。qMGR 可以进一步检测分类单元内的保守基因集和高频重排片段。它们可能有助于评估重排距离和理解重排机制。qMGR 网络服务可在 http://qmgr.hnnu.edu.cn/ 免费获得。源代码可在 GNU GPL 下获得，网址为 https://github.com/zhanglab2019/qMGR。qMGR 可以进一步检测分类单元内的保守基因集和高频重排片段。它们可能有助于评估重排距离和理解重排机制。qMGR 网络服务可在 http://qmgr.hnnu.edu.cn/ 免费获得。源代码可在 GNU GPL 下获得，网址为 https://github.com/zhanglab2019/qMGR。