4.7 Article

PaReBrick: PArallel REarrangements and BReaks identification toolkit

期刊

BIOINFORMATICS
卷 38, 期 2, 页码 357-363

出版社

OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/btab691

关键词

-

资金

  1. National Center for Cognitive Research of ITMO University
  2. European Union's Horizon 2020 Research and Innovation Programme [754411]
  3. JetBrains Research

向作者/读者索取更多资源

The study defines "parallel rearrangements" and presents a formalization of the problem of parallel rearrangements calling. An algorithmic solution called PaReBrick is implemented for identifying parallel rearrangements in bacterial populations, demonstrating efficiency and accuracy in detecting genome rearrangements responsible for pathogenicity and adaptation.
Motivation: High plasticity of bacterial genomes is provided by numerous mechanisms including horizontal gene transfer and recombination via numerous flanking repeats. Genome rearrangements such as inversions, deletions, insertions and duplications may independently occur in different strains, providing parallel adaptation or phenotypic diversity. Specifically, such rearrangements might be responsible for virulence, antibiotic resistance and antigenic variation. However, identification of such events requires laborious manual inspection and verification of phyletic pattern consistency. Results: Here, we define the term 'parallel rearrangements' as events that occur independently in phylogenetically distant bacterial strains and present a formalization of the problem of parallel rearrangements calling. We implement an algorithmic solution for the identification of parallel rearrangements in bacterial populations as a tool PaReBrick. The tool takes a collection of strains represented as a sequence of oriented synteny blocks and a phylogenetic tree as input data. It identifies rearrangements, tests them for consistency with a tree, and sorts the events by their parallelism score. The tool provides diagrams of the neighbors for each block of interest, allowing the detection of horizontally transferred blocks or their extra copies and the inversions in which copied blocks are involved. We demonstrated PaReBrick's efficiency and accuracy and showed its potential to detect genome rearrangements responsible for pathogenicity and adaptation in bacterial genomes.

作者

我是这篇论文的作者
点击您的名字以认领此论文并将其添加到您的个人资料中。

评论

主要评分

4.7
评分不足

次要评分

新颖性
-
重要性
-
科学严谨性
-
评价这篇论文

推荐

暂无数据
暂无数据