{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,13]],"date-time":"2026-04-13T06:40:59Z","timestamp":1776062459779,"version":"3.50.1"},"reference-count":17,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2021,10,3]],"date-time":"2021-10-03T00:00:00Z","timestamp":1633219200000},"content-version":"vor","delay-in-days":1,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"National Center for Cognitive Research of ITMO University and JetBrains Research"},{"name":"European Union\u2019s Horizon 2020 Research and Innovation Programme under the Marie Sk\u0142odowska-Curie","award":["754411"],"award-info":[{"award-number":["754411"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,1,3]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>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.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Here, we define the term \u2018parallel rearrangements\u2019 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\u2019s efficiency and accuracy and showed its potential to detect genome rearrangements responsible for pathogenicity and adaptation in bacterial genomes.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>PaReBrick is written in Python and is available on GitHub: https:\/\/github.com\/ctlab\/parallel-rearrangements.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btab691","type":"journal-article","created":{"date-parts":[[2021,9,30]],"date-time":"2021-09-30T12:18:42Z","timestamp":1633004322000},"page":"357-363","source":"Crossref","is-referenced-by-count":8,"title":["PaReBrick: PArallel REarrangements and BReaks identification toolkit"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5433-0150","authenticated-orcid":false,"given":"Alexey","family":"Zabelkin","sequence":"first","affiliation":[{"name":"Computer Technologies Laboratory, ITMO University , St Petersburg 197101, Russia"},{"name":"Bioinformatics Institute , St Petersburg 194100, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0202-7245","authenticated-orcid":false,"given":"Yulia","family":"Yakovleva","sequence":"additional","affiliation":[{"name":"Bioinformatics Institute , St Petersburg 194100, Russia"},{"name":"Department of Microbiology, Faculty of Biology, Saint Petersburg State University, St Petersburg 199034, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1006-6639","authenticated-orcid":false,"given":"Olga","family":"Bochkareva","sequence":"additional","affiliation":[{"name":"Institute of Science and Technology (IST Austria) , 3400 Klosterneuburg, Austria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3415-9565","authenticated-orcid":false,"given":"Nikita","family":"Alexeev","sequence":"additional","affiliation":[{"name":"Computer Technologies Laboratory, ITMO University , St Petersburg 197101, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2021,10,2]]},"reference":[{"key":"2023020108464070300_btab691-B1","doi-asserted-by":"crossref","first-page":"965","DOI":"10.1186\/s12864-018-5245-1","article-title":"Genome rearrangements and selection in multi-chromosome bacteria Burkholderia spp","volume":"19","author":"Bochkareva","year":"2018","journal-title":"BMC Genomics"},{"key":"2023020108464070300_btab691-B2","doi-asserted-by":"crossref","first-page":"e1008615","DOI":"10.1371\/journal.pgen.1008615","article-title":"The snap hypothesis: chromosomal rearrangements could emerge from positive selection during niche adaptation","volume":"16","author":"Brandis","year":"2020","journal-title":"PLoS Genet"},{"key":"2023020108464070300_btab691-B3","doi-asserted-by":"crossref","first-page":"e1000128","DOI":"10.1371\/journal.pgen.1000128","article-title":"Dynamics of genome rearrangement in bacterial populations","volume":"4","author":"Darling","year":"2008","journal-title":"PLoS Genet"},{"key":"2023020108464070300_btab691-B4","doi-asserted-by":"crossref","first-page":"e47768","DOI":"10.1371\/journal.pone.0047768","article-title":"Mind the gap: upgrading genomes with pacific biosciences rs long-read sequencing technology","volume":"7","author":"English","year":"2012","journal-title":"PLoS One"},{"key":"2023020108464070300_btab691-B5","doi-asserted-by":"crossref","first-page":"406","DOI":"10.2307\/2412116","article-title":"Toward defining the course of evolution: minimum change for a specific tree topology","volume":"20","author":"Fitch","year":"1971","journal-title":"Syst. Zool"},{"key":"2023020108464070300_btab691-B6","doi-asserted-by":"crossref","first-page":"20135","DOI":"10.1073\/pnas.1904861116","article-title":"Unstable chromosome rearrangements in Staphylococcus aureus cause phenotype switching associated with persistent infections","volume":"116","author":"Gu\u00e9rillot","year":"2019","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2023020108464070300_btab691-B7","doi-asserted-by":"crossref","first-page":"11468","DOI":"10.1093\/nar\/gkaa907","article-title":"Prevalence of phase variable epigenetic invertons among host-associated bacteria","volume":"48","author":"Huang","year":"2020","journal-title":"Nucleic Acids Res"},{"key":"2023020108464070300_btab691-B8","doi-asserted-by":"crossref","first-page":"e000262","DOI":"10.1099\/mgen.0.000262","article-title":"Genomic and transcriptomic characterization of Pseudomonas aeruginosa small colony variants derived from a chronic infection model","volume":"5","author":"Irvine","year":"2019","journal-title":"Microb. Genomics"},{"key":"2023020108464070300_btab691-B9","doi-asserted-by":"crossref","first-page":"i302","DOI":"10.1093\/bioinformatics\/btu280","article-title":"Ragout\u2013a reference-assisted assembly tool for bacterial genomes","volume":"30","author":"Kolmogorov","year":"2014","journal-title":"Bioinformatics"},{"key":"2023020108464070300_btab691-B10","doi-asserted-by":"crossref","first-page":"327","DOI":"10.1186\/s12864-015-1519-z","article-title":"Genome assembly using nanopore-guided long and error-free DNA reads","volume":"16","author":"Madoui","year":"2015","journal-title":"BMC Genomics"},{"key":"2023020108464070300_btab691-B11","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41467-020-19777-8","article-title":"Scalable multiple whole-genome alignment and locally collinear block construction with SibeliaZ","volume":"11","author":"Minkin","year":"2020","journal-title":"Nat. Commun"},{"key":"2023020108464070300_btab691-B12","first-page":"lqaa106","article-title":"PanACoTA: a modular tool for massive microbial comparative genomics","volume":"3","author":"Perrin","year":"2021","journal-title":"NAR Genomics Bioinf"},{"key":"2023020108464070300_btab691-B13","doi-asserted-by":"crossref","first-page":"1902","DOI":"10.1093\/molbev\/msx127","article-title":"Non-random inversion landscapes in prokaryotic genomes are shaped by heterogeneous selection pressures","volume":"34","author":"Repar","year":"2017","journal-title":"Mol. Biol. Evol"},{"key":"2023020108464070300_btab691-B14","doi-asserted-by":"crossref","first-page":"628622","DOI":"10.3389\/fmicb.2021.628622","article-title":"High rates of genome rearrangements and pathogenicity of Shigella spp","volume":"12","author":"Seferbekova","year":"2021","journal-title":"Front. Microbiol"},{"key":"2023020108464070300_btab691-B15","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1186\/s12862-019-1403-6","article-title":"Micro-evolution of three Streptococcus species: selection, antigenic variation, and horizontal gene inflow","volume":"19","author":"Shelyakin","year":"2019","journal-title":"BMC Evol. Biol"},{"key":"2023020108464070300_btab691-B16","first-page":"9971","article-title":"Deep genome annotation of the opportunistic human pathogen Streptococcus pneumoniae d39","volume":"46","author":"Slager","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"2023020108464070300_btab691-B17","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1016\/j.tig.2020.09.004","article-title":"Site-specific recombination \u2013 how simple DNA inversions produce complex phenotypic heterogeneity in bacterial populations","volume":"37","author":"Trzilova","year":"2021","journal-title":"Trends Genet"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btab691\/41099137\/btab691.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/38\/2\/357\/49007313\/btab691.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/38\/2\/357\/49007313\/btab691.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,1]],"date-time":"2023-02-01T15:03:09Z","timestamp":1675263789000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/38\/2\/357\/6380551"}},"subtitle":[],"editor":[{"given":"Russell","family":"Schwartz","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2021,10,2]]},"references-count":17,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2022,1,3]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btab691","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2021.05.18.444676","asserted-by":"object"}]},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2022,1,15]]},"published":{"date-parts":[[2021,10,2]]}}}