This paper generalizes previous studies on genome rearrangement under biological constraints, using double cut and join (DCJ). We propose a model for weighted DCJ, along with a family of optimization problems called φ -MCPS (Minimum Cost Parsimonious Scenario), that are based on labeled graphs. We show how to compute solutions to general instances of φ -MCPS, given an algorithm to compute φ -MCPS on a circular genome with exactly one occurrence of each gene. These general instances can have an arbitrary number of circular and linear chromosomes, and arbitrary gene content. The practicality of the framework is displayed by presenting polynomial-time algorithms that generalize the results of Bulteau, Fertin, and Tannier on the Sorting by wDCJs and indels in intergenes problem, and that generalize previous results on the Minimum Local Parsimonious Scenario problem.

中文翻译：

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具有生物学限制的基因组重排的一般框架。

本文概括了以前在生物学限制下使用双切和连接（DCJ）技术进行基因组重排的研究。我们提出了基于标签图的加权DCJ模型，以及一系列称为φ-MCPS（最小成本简约方案）的优化问题。我们给出了一种算法，它给出了一种在圆形基因组上计算φ-MCPS的算法，每个基因恰好出现一次，从而说明了如何计算φ-MCPS的一般实例的解决方案。这些一般实例可以具有任意数量的圆形和线性染色体，以及任意的基因含量。通过提出多项式时间算法来展示该框架的实用性，该算法可以将Bulteau，Fertin和Tannier的结果推广到基因间问题中的wDCJ和indel的排序上，