采用双切割与连接的基因组二等分

Genome aliquoting with double cut and join.

作者信息

Warren Robert, Sankoff David

机构信息

School of Information Technology and Engineering, University of Ottawa, 800 King Edward Avenue, Ottawa, Canada.

出版信息

BMC Bioinformatics. 2009 Jan 30;10 Suppl 1(Suppl 1):S2. doi: 10.1186/1471-2105-10-S1-S2.

DOI:10.1186/1471-2105-10-S1-S2

PMID:19208119

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC2648758/

Abstract

BACKGROUND

The genome aliquoting problem is, given an observed genome A with n copies of each gene, presumed to descend from an n-way polyploidization event from an ordinary diploid genome B, followed by a history of chromosomal rearrangements, to reconstruct the identity of the original genome B'. The idea is to construct B', containing exactly one copy of each gene, so as to minimize the number of rearrangements d(A, B' plus sign in circle B' plus sign in circle ... plus sign in circle B') necessary to convert the observed genome B' plus sign in circle B' plus sign in circle ... plus sign in circle B' into A.

RESULTS

In this paper we make the first attempt to define and solve the genome aliquoting problem. We present a heuristic algorithm for the problem as well the data from our experiments demonstrating its validity.

CONCLUSION

The heuristic performs well, consistently giving a non-trivial result. The question as to the existence or non-existence of an exact solution to this problem remains open.

摘要

背景

基因组二等分问题是，给定一个观察到的基因组A，其中每个基因有n个拷贝，假定它源自普通二倍体基因组B的n倍多倍体化事件，随后经历了染色体重排历史，要重建原始基因组B'的身份。其思路是构建B'，其中每个基因恰好有一个拷贝，以使将观察到的基因组B'⊕B'⊕...⊕B'转换为A所需的重排数d(A, B'⊕B'⊕...⊕B')最小化。