一个基于Double Cut and Join的代价约束基因组重排框架
A framework for cost-constrained genome rearrangement under Double Cut and Join
摘要：
基因组重排的研究有很多种，但它们都与称为断点图的多图的变化上的编辑距离有关。我们研究了欧拉2-边着色多重图的加权2-断点距离，它推广了几个双割和连接问题的加权版本，包括基因含量不等的基因组。我们肯定循环分解和编辑场景之间的连接，首先发现与排序的逆转问题。利用这一点，我们表明，找到一个简约的情况下的最小成本的欧拉2-边着色的多重图的问题-与一般的成本函数为2-休息-可以通过分解成简单的交替循环的独立实例的问题得到解决。对于断点图，和一个更受约束的成本函数，着色的顶点的基础上，我们给出了一个多项式时间算法找到一个最小成本的简约2-断点的情况下，同时表明，找到一个非简约的2-断点的情况下，最小成本是NP-难的。
英文摘要：
The study of genome rearrangement has many flavours, but they all are somehow tied to edit distances on variations of a multi-graph called the breakpoint graph. We study a weighted 2-break distance on Eulerian 2-edge-colored multi-graphs, which generalizes weighted versions of several Double Cut and Join problems, including those on genomes with unequal gene content. We affirm the connection between cycle decompositions and edit scenarios first discovered with the Sorting By Reversals problem. Using this we show that the problem of finding a parsimonious scenario of minimum cost on an Eulerian 2-edge-colored multi-graph - with a general cost function for 2-breaks - can be solved by decomposing the problem into independent instances on simple alternating cycles. For breakpoint graphs, and a more constrained cost function, based on coloring the vertices, we give a polynomial-time algorithm for finding a parsimonious 2-break scenario of minimum cost, while showing that finding a non-parsimonious 2-break scenario of minimum cost is NP-Hard.
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