{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,24]],"date-time":"2026-01-24T16:32:23Z","timestamp":1769272343265,"version":"3.49.0"},"reference-count":25,"publisher":"Oxford University Press (OUP)","issue":"22","license":[{"start":{"date-parts":[[2018,6,20]],"date-time":"2018-06-20T00:00:00Z","timestamp":1529452800000},"content-version":"vor","delay-in-days":1,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100004508","name":"Prince of Songkla University","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004508","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,11,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>The advent of next-generation sequencing has boosted the analysis of bacterial genome evolution. Insertion sequence (IS) elements play a key role in prokaryotic genome organization and evolution, but their repetitions in genomes complicate their detection from short-read data.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>PanISa is a software pipeline that identifies IS insertions ab initio in bacterial genomes from short-read data. It is a highly sensitive and precise tool based on the detection of read-mapping patterns at the insertion site. PanISa performs better than existing IS detection systems as it is based on a database-free approach. We applied it to a high-risk clone lineage of the pathogenic species Pseudomonas aeruginosa, and report 43 insertions of five different ISs (among which three are new) and a burst of ISPa1635 in a hypermutator isolate.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>PanISa is implemented in Python and released as an open source software (GPL3) at https:\/\/github.com\/bvalot\/panISa.<\/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\/bty479","type":"journal-article","created":{"date-parts":[[2018,6,13]],"date-time":"2018-06-13T19:13:00Z","timestamp":1528917180000},"page":"3795-3800","source":"Crossref","is-referenced-by-count":40,"title":["<i>panISa: ab initio<\/i> detection of insertion sequences in bacterial genomes from short read sequence data"],"prefix":"10.1093","volume":"34","author":[{"given":"Panisa","family":"Treepong","sequence":"first","affiliation":[{"name":"D\u00e9partement DISC, UMR CNRS 6174 Institut FEMTO-ST, Universit\u00e9 de Bourgogne, Franche-Comt\u00e9, Besan\u00e7on, France"},{"name":"Faculty of Technology and Environment, Prince of Songkla University, Phuket, Thailand"}]},{"given":"Christophe","family":"Guyeux","sequence":"additional","affiliation":[{"name":"D\u00e9partement DISC, UMR CNRS 6174 Institut FEMTO-ST, Universit\u00e9 de Bourgogne, Franche-Comt\u00e9, Besan\u00e7on, France"}]},{"given":"Alexandre","family":"Meunier","sequence":"additional","affiliation":[{"name":"Laboratoire d\u2019Hygi\u00e8ne Hospitali\u00e8re, Centre Hospitalier R\u00e9gional Universitaire, Besan\u00e7on, France"},{"name":"UMR CNRS 6249, Chrono-environnement, Universit\u00e9 de Bourgogne Franche-Comt\u00e9, Besan\u00e7on, France"}]},{"given":"Charlotte","family":"Couchoud","sequence":"additional","affiliation":[{"name":"Laboratoire d\u2019Hygi\u00e8ne Hospitali\u00e8re, Centre Hospitalier R\u00e9gional Universitaire, Besan\u00e7on, France"}]},{"given":"Didier","family":"Hocquet","sequence":"additional","affiliation":[{"name":"Laboratoire d\u2019Hygi\u00e8ne Hospitali\u00e8re, Centre Hospitalier R\u00e9gional Universitaire, Besan\u00e7on, France"},{"name":"UMR CNRS 6249, Chrono-environnement, Universit\u00e9 de Bourgogne Franche-Comt\u00e9, Besan\u00e7on, France"}]},{"given":"Benoit","family":"Valot","sequence":"additional","affiliation":[{"name":"UMR CNRS 6249, Chrono-environnement, Universit\u00e9 de Bourgogne Franche-Comt\u00e9, Besan\u00e7on, France"}]}],"member":"286","published-online":{"date-parts":[[2018,6,19]]},"reference":[{"key":"2023012712290624200_bty479-B1","doi-asserted-by":"crossref","first-page":"1039","DOI":"10.1186\/1471-2164-15-1039","article-title":"Identifying structural variation in haploid microbial genomes from short-read resequencing data using breseq","volume":"15","author":"Barrick","year":"2014","journal-title":"BMC Genomics"},{"key":"2023012712290624200_bty479-B2","doi-asserted-by":"crossref","first-page":"1519","DOI":"10.1089\/cmb.2009.0238","article-title":"Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies","volume":"17","author":"Boisvert","year":"2010","journal-title":"J. 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