---
_id: '10927'
abstract:
- lang: eng
  text: "Motivation\r\nHigh 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.\r\nResults\r\nHere, 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."
acknowledgement: "The authors thank the 2020 student class of the Bioinformatics Institute,
  who\r\nused the first versions of the tool and provided many valuable suggestions
  to\r\nimprove usability. They also thank Louisa Gonzalez Somermeyer for manuscript
  proofreading\r\nThis work was supported by the National Center for Cognitive Research
  of\r\nITMO University and JetBrains Research [to A.Z and N.A.]; and the European\r\nUnion’s
  Horizon 2020 Research and Innovation Programme under the Marie\r\nSkłodowska-Curie
  [754411 to O.B.].\r\nPaReBrick is written in Python and is available on GitHub:
  https://github.com/ctlab/parallel-rearrangements."
article_processing_charge: No
article_type: original
author:
- first_name: Alexey
  full_name: Zabelkin, Alexey
  last_name: Zabelkin
- first_name: Yulia
  full_name: Yakovleva, Yulia
  last_name: Yakovleva
- first_name: Olga
  full_name: Bochkareva, Olga
  id: C4558D3C-6102-11E9-A62E-F418E6697425
  last_name: Bochkareva
  orcid: 0000-0003-1006-6639
- first_name: Nikita
  full_name: Alexeev, Nikita
  last_name: Alexeev
citation:
  ama: 'Zabelkin A, Yakovleva Y, Bochkareva O, Alexeev N. PaReBrick: PArallel REarrangements
    and BReaks identification toolkit. <i>Bioinformatics</i>. 2022;38(2):357-363.
    doi:<a href="https://doi.org/10.1093/bioinformatics/btab691">10.1093/bioinformatics/btab691</a>'
  apa: 'Zabelkin, A., Yakovleva, Y., Bochkareva, O., &#38; Alexeev, N. (2022). PaReBrick:
    PArallel REarrangements and BReaks identification toolkit. <i>Bioinformatics</i>.
    Oxford University Press. <a href="https://doi.org/10.1093/bioinformatics/btab691">https://doi.org/10.1093/bioinformatics/btab691</a>'
  chicago: 'Zabelkin, Alexey, Yulia Yakovleva, Olga Bochkareva, and Nikita Alexeev.
    “PaReBrick: PArallel REarrangements and BReaks Identification Toolkit.” <i>Bioinformatics</i>.
    Oxford University Press, 2022. <a href="https://doi.org/10.1093/bioinformatics/btab691">https://doi.org/10.1093/bioinformatics/btab691</a>.'
  ieee: 'A. Zabelkin, Y. Yakovleva, O. Bochkareva, and N. Alexeev, “PaReBrick: PArallel
    REarrangements and BReaks identification toolkit,” <i>Bioinformatics</i>, vol.
    38, no. 2. Oxford University Press, pp. 357–363, 2022.'
  ista: 'Zabelkin A, Yakovleva Y, Bochkareva O, Alexeev N. 2022. PaReBrick: PArallel
    REarrangements and BReaks identification toolkit. Bioinformatics. 38(2), 357–363.'
  mla: 'Zabelkin, Alexey, et al. “PaReBrick: PArallel REarrangements and BReaks Identification
    Toolkit.” <i>Bioinformatics</i>, vol. 38, no. 2, Oxford University Press, 2022,
    pp. 357–63, doi:<a href="https://doi.org/10.1093/bioinformatics/btab691">10.1093/bioinformatics/btab691</a>.'
  short: A. Zabelkin, Y. Yakovleva, O. Bochkareva, N. Alexeev, Bioinformatics 38 (2022)
    357–363.
corr_author: '1'
date_created: 2022-03-27T22:01:46Z
date_published: 2022-01-15T00:00:00Z
date_updated: 2025-05-14T11:05:09Z
day: '15'
ddc:
- '000'
department:
- _id: FyKo
doi: 10.1093/bioinformatics/btab691
ec_funded: 1
external_id:
  isi:
  - '000743380100008'
file:
- access_level: open_access
  checksum: 4b5688ff9ac86180ccdf7f82fa33d926
  content_type: application/pdf
  creator: dernst
  date_created: 2022-03-28T08:07:46Z
  date_updated: 2022-03-28T08:07:46Z
  file_id: '10930'
  file_name: 2022_Bioinformatics_Zabelkin.pdf
  file_size: 3425744
  relation: main_file
  success: 1
file_date_updated: 2022-03-28T08:07:46Z
has_accepted_license: '1'
intvolume: '        38'
isi: 1
issue: '2'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 357-363
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '754411'
  name: ISTplus - Postdoctoral Fellowships
publication: Bioinformatics
publication_identifier:
  eissn:
  - 1460-2059
  issn:
  - 1367-4803
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
related_material:
  link:
  - relation: software
    url: https://github.com/ctlab/parallel-rearrangements
scopus_import: '1'
status: public
title: 'PaReBrick: PArallel REarrangements and BReaks identification toolkit'
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 38
year: '2022'
...