{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,17]],"date-time":"2026-04-17T17:56:30Z","timestamp":1776448590765,"version":"3.51.2"},"reference-count":17,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2020,9,21]],"date-time":"2020-09-21T00:00:00Z","timestamp":1600646400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Vetenskapsr\u00e5det (the Swedish Research Council","award":["2015-04746"],"award-info":[{"award-number":["2015-04746"]}]},{"name":"Vetenskapsr\u00e5det (the Swedish Research Council","award":["2019-01085"],"award-info":[{"award-number":["2019-01085"]}]},{"name":"Ume\u00e5 University Medical Faculty"},{"name":"Ume\u00e5 Centre of Microbial Research (UCMR) Linnaeus Program Gender Policy Support"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,6,9]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Analysis of conservation of gene neighbourhoods over different evolutionary levels is important for understanding operon and gene cluster evolution, and predicting functional associations. Our tool FlaGs (standing for Flanking Genes) takes a list of NCBI protein accessions as input, clusters neighbourhood-encoded proteins into homologous groups using sensitive sequence searching, and outputs a graphical visualization of the gene neighbourhood and its conservation, along with a phylogenetic tree annotated with flanking gene conservation. FlaGs has demonstrated utility for molecular evolutionary analysis, having uncovered a new toxin\u2013antitoxin system in prokaryotes and bacteriophages. The web tool version of FlaGs (webFlaGs) can optionally include a BLASTP search against a reduced RefSeq database to generate an input accession list and analyse neighbourhood conservation within the same run.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>FlaGs can be downloaded from https:\/\/github.com\/GCA-VH-lab\/FlaGs or run online at http:\/\/www.webflags.se\/.<\/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\/btaa788","type":"journal-article","created":{"date-parts":[[2020,9,8]],"date-time":"2020-09-08T19:13:50Z","timestamp":1599592430000},"page":"1312-1314","source":"Crossref","is-referenced-by-count":162,"title":["FlaGs and webFlaGs: discovering novel biology through the analysis of gene neighbourhood conservation"],"prefix":"10.1093","volume":"37","author":[{"given":"Chayan Kumar","family":"Saha","sequence":"first","affiliation":[{"name":"Department of Molecular Biology and Ume\u00e5 Centre for Microbial Research , Ume\u00e5 University, Ume\u00e5 901 87, Sweden"}]},{"given":"Rodrigo","family":"Sanches Pires","sequence":"additional","affiliation":[{"name":"Department of Chemistry, KTH Royal Institute of Technology , Stockholm 100 44, Sweden"}]},{"given":"Harald","family":"Brolin","sequence":"additional","affiliation":[{"name":"Department of Molecular and Clinical Medicine, Wallenberg Laboratory, University of Gothenburg , Gothenburg 413 45, Sweden"}]},{"given":"Maxence","family":"Delannoy","sequence":"additional","affiliation":[{"name":"D\u00e9partement G\u00e9nie Biologique, Campus SophiaTech, Universit\u00e9 Nice Sophia Antipolis , Nice 06900, France"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4861-4584","authenticated-orcid":false,"given":"Gemma Catherine","family":"Atkinson","sequence":"additional","affiliation":[{"name":"Department of Molecular Biology and Ume\u00e5 Centre for Microbial Research , Ume\u00e5 University, Ume\u00e5 901 87, Sweden"}]}],"member":"286","published-online":{"date-parts":[[2020,12,12]]},"reference":[{"key":"2023051705213036100_btaa788-B1","doi-asserted-by":"crossref","first-page":"421","DOI":"10.1186\/1471-2105-10-421","article-title":"BLAST+: architecture and applications","volume":"10","author":"Camacho","year":"2009","journal-title":"BMC Bioinformatics"},{"key":"2023051705213036100_btaa788-B2","doi-asserted-by":"crossref","first-page":"324","DOI":"10.1016\/S0968-0004(98)01274-2","article-title":"Conservation of gene order: a fingerprint of proteins that physically interact","volume":"23","author":"Dandekar","year":"1998","journal-title":"Trends Biochem. 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