{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,4]],"date-time":"2026-08-04T11:32:34Z","timestamp":1785843154419,"version":"3.56.0"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2018,6,15]],"date-time":"2018-06-15T00:00:00Z","timestamp":1529020800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"French ANR","award":["ANR-16-CE02-0005"],"award-info":[{"award-number":["ANR-16-CE02-0005"]}]},{"DOI":"10.13039\/501100010115","name":"Region Auvergne Rh\u00f4ne-Alpes","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100010115","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,1,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>The exploration and comparison of genome organization is routinely used in the frame of genomic and phylogenomic analyses. As a consequence, in the past few years, various tools allowing visualizing genomic contexts have been developed. However, their use is often hampered by a lack of flexibility, particularly concerning associated databases input formats and figure customization. Here we present GeneSpy, a graphical user interface that allows the visualization and dynamic exploration of eukaryotic and prokaryotic annotated genomes. GeneSpy relies on user-friendly manageable local databases and allows the easy customization and production of figures in a multitude of formats.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>GeneSpy is freely available at https:\/\/lbbe.univ-lyon1.fr\/GeneSpy\/ for Linux, Mac OS and Windows under CeCILL license (http:\/\/www.cecill.info\/licences\/). It is written in Python 2.7 and depends on Matplotlib, Tkinter and Sqlite libraries.<\/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\/bty459","type":"journal-article","created":{"date-parts":[[2018,6,12]],"date-time":"2018-06-12T11:09:38Z","timestamp":1528801778000},"page":"329-331","source":"Crossref","is-referenced-by-count":52,"title":["GeneSpy, a user-friendly and flexible genomic context visualizer"],"prefix":"10.1093","volume":"35","author":[{"given":"Pierre Simon","family":"Garcia","sequence":"first","affiliation":[{"name":"Univ Lyon, Universit\u00e9 Lyon 1, CNRS, UMR5558, Laboratoire de Biom\u00e9trie et Biologie \u00c9volutive, Villeurbanne, France"},{"name":"MMSB Molecular Microbiology and Structural Biochemistry, Institut de Biologie et de Chimie des Prot\u00e9ines 7 passage du Vercors, LYON cedex, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fr\u00e9d\u00e9ric","family":"Jauffrit","sequence":"additional","affiliation":[{"name":"Univ Lyon, Universit\u00e9 Lyon 1, CNRS, UMR5558, Laboratoire de Biom\u00e9trie et Biologie \u00c9volutive, Villeurbanne, France"},{"name":"R&D microbiology, Clinical Unit, bioMerieux, Marcy L'Etoile, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christophe","family":"Grangeasse","sequence":"additional","affiliation":[{"name":"MMSB Molecular Microbiology and Structural Biochemistry, Institut de Biologie et de Chimie des Prot\u00e9ines 7 passage du Vercors, LYON cedex, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"C\u00e9line","family":"Brochier-Armanet","sequence":"additional","affiliation":[{"name":"Univ Lyon, Universit\u00e9 Lyon 1, CNRS, UMR5558, Laboratoire de Biom\u00e9trie et Biologie \u00c9volutive, Villeurbanne, France"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2018,6,15]]},"reference":[{"key":"2023013107233226900_bty459-B1","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1186\/1471-2164-9-75","article-title":"The RAST Server: rapid annotations using subsystems technology","volume":"9","author":"Aziz","year":"2008","journal-title":"BMC Genomics"},{"key":"2023013107233226900_bty459-B2","doi-asserted-by":"crossref","first-page":"529","DOI":"10.1016\/S0168-9525(00)02142-9","article-title":"The evolutionary history of ribosomal protein RpS14: horizontal gene transfer at the heart of the ribosome","volume":"16","author":"Brochier","year":"2000","journal-title":"Trends Genet"},{"key":"2023013107233226900_bty459-B3","doi-asserted-by":"crossref","first-page":"W242","DOI":"10.1093\/nar\/gkw290","article-title":"Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other 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