无基因家族中位数为3
The gene family-free median of three
摘要：
比较基因组学的无基因家族框架旨在开发不需要事先指定基因家族，而是直接在序列相似性多部图上工作的基因顺序分析方法。我们提出了一个模型，用于构建一个中位数的三个基因组在这个家庭的自由设置，基于最大化的目标函数，概括了经典的断点距离，通过整合序列相似性的得分的基因邻接。我们证明了相应的计算问题是MAX SNP-困难的，我们提出了一个0 - 1线性规划的精确解。我们的FF-中值程序的结果是中值基因组与现存基因相关，其中中值邻接被假设为定义位置直系同源物。我们证明，通过模拟和比较与OMA的直系同源数据库，本文提出的方法是能够计算准确的中位数和位置的直系同源的基因组可比的细菌基因组的大小。
英文摘要：
The gene family-free framework for comparative genomics aims at developing methods for gene order analysis that do not require prior gene family assignment, but work directly on a sequence similarity multipartite graph. We present a model for constructing a median of three genomes in this family-free setting, based on maximizing an objective function that generalizes the classical breakpoint distance by integrating sequence similarity in the score of a gene adjacency. We show that the corresponding computational problem is MAX SNP-hard and we present a 0-1 linear program for its exact solution. The result of our FF-median program is a median genome with median genes associated to extant genes, in which median adjacencies are assumed to define positional orthologs. We demonstrate through simulations and comparison with the OMA orthology database that the herein presented method is able compute accurate medians and positional orthologs for genomes comparable in size of bacterial genomes.
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