自然无家系基因组距离
Natural family-free genomic distance
摘要：
比较基因组学中的一个经典问题是计算重排距离，即将一个给定的基因组转化为另一个给定的基因组所需的大规模重排的最小数量。虽然这方面最传统的办法是以家庭为基础，需要将DNA片段分类到家族中，最近提出了一种替代的无家族方法，并且包括在没有预先家族分配的情况下研究重排距离。一方面，在无家族背景下计算基因组距离有助于匹配重复基因的出现并找到同源性，但另一方面，这种计算是NP难的。本文提出了一种新的、更一般的无家族基因组距离的概念，即用通用的双切割和连接（DCJ）操作来表示结构重排，并允许DNA片段的插入和缺失，从而提供了一种有效的ILP公式来求解该问题.实验表明，该ILP算法不仅能处理细菌基因组，而且能处理真菌和昆虫基因组，或哺乳动物和植物染色体的子集。
英文摘要：
A classical problem in comparative genomics is to compute the rearrangement distance, that is the minimum number of large-scale rearrangements required to transform a given genome into another given genome. While the most traditional approaches in this area are family-based, i.e., require the classification of DNA fragments into families, more recently an alternative family-free approach was proposed, and consists of studying the rearrangement distances without prior family assignment. On the one hand the computation of genomic distances in the family-free setting helps to match occurrences of duplicated genes and find homologies, but on the other hand this computation is NP-hard. In this paper, by letting structural rearrangements be represented by the generic double cut and join (DCJ) operation and also allowing insertions and deletions of DNA segments, we propose a new and more general family-free genomic distance, providing an efficient ILP formulation to solve it. Our experiments show that the ILP produces accurate results and can handle not only bacterial genomes, but also fungi and insects, or subsets of chromosomes of mammals and plants.
机构、总结、中文摘要均由AI分析而来，可能存在错误，请以论文正文为准。
