{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,24]],"date-time":"2026-06-24T16:16:49Z","timestamp":1782317809095,"version":"3.54.5"},"reference-count":14,"publisher":"Oxford University Press (OUP)","issue":"17","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: We have developed CiVi, a user-friendly web-based tool to create custom circular maps to aid the analysis of microbial genomes and sequence elements. Sequence related data such as gene-name, COG class, PFAM domain, GC%, and subcellular location can be comprehensively viewed. Quantitative gene-related data (e.g. expression ratios or read counts) as well as predicted sequence elements (e.g. regulatory sequences) can be uploaded and visualized. CiVi accommodates the analysis of genomic elements by allowing a visual interpretation in the context of: (i) their genome-wide distribution, (ii) provided experimental data and (iii) the local orientation and location with respect to neighboring genes. CiVi thus enables both experts and non-experts to conveniently integrate public genome data with the results of genome analyses in circular genome maps suitable for publication.<\/jats:p>\n               <jats:p>Contact: \u00a0L.Overmars@gmail.com<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <jats:p>Availability and implementation: CiVi is freely available at http:\/\/civi.cmbi.ru.nl<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv249","type":"journal-article","created":{"date-parts":[[2015,4,25]],"date-time":"2015-04-25T01:51:42Z","timestamp":1429926702000},"page":"2867-2869","source":"Crossref","is-referenced-by-count":35,"title":["CiVi: circular genome visualization with unique features to analyze sequence elements"],"prefix":"10.1093","volume":"31","author":[{"given":"Lex","family":"Overmars","sequence":"first","affiliation":[{"name":"1 CMBI, Radboud University Medical Centre, Nijmegen 6525GA, The Netherlands,"},{"name":"2 Netherlands Bioinformatics Centre, Nijmegen 6500HB, The Netherlands,"},{"name":"3 Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands,"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sacha A. F. T.","family":"van Hijum","sequence":"additional","affiliation":[{"name":"1 CMBI, Radboud University Medical Centre, Nijmegen 6525GA, The Netherlands,"},{"name":"2 Netherlands Bioinformatics Centre, Nijmegen 6500HB, The Netherlands,"},{"name":"4 NIZO Food Research B.V., Ede, The Netherlands and"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Roland J.","family":"Siezen","sequence":"additional","affiliation":[{"name":"1 CMBI, Radboud University Medical Centre, Nijmegen 6525GA, The Netherlands,"},{"name":"2 Netherlands Bioinformatics Centre, Nijmegen 6500HB, The Netherlands,"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christof","family":"Francke","sequence":"additional","affiliation":[{"name":"1 CMBI, Radboud University Medical Centre, Nijmegen 6525GA, The Netherlands,"},{"name":"2 Netherlands Bioinformatics Centre, Nijmegen 6500HB, The Netherlands,"},{"name":"5 Hogeschool Arnhem en Nijmegen BioCentre, 6525EM Nijmegen, The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2015,4,24]]},"reference":[{"key":"2023020202234386100_btv249-B1","doi-asserted-by":"crossref","first-page":"402","DOI":"10.1186\/1471-2164-12-402","article-title":"BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons","volume":"12","author":"Alikhan","year":"2011","journal-title":"BMC Genomics"},{"key":"2023020202234386100_btv249-B2","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1093\/bioinformatics\/btn578","article-title":"DNAPlotter: circular and linear interactive genome visualization","volume":"25","author":"Carver","year":"2009","journal-title":"Bioinformatics"},{"key":"2023020202234386100_btv249-B3","doi-asserted-by":"crossref","first-page":"861","DOI":"10.1093\/bioinformatics\/btm598","article-title":"GenomeVx: simple web-based creation of editable circular chromosome maps","volume":"24","author":"Conant","year":"2008","journal-title":"Bioinformatics"},{"key":"2023020202234386100_btv249-B4","doi-asserted-by":"crossref","first-page":"3125","DOI":"10.1093\/bioinformatics\/btu505","article-title":"Circleator: flexible circular visualization of genome-associated data with BioPerl and SVG","volume":"30","author":"Crabtree","year":"2014","journal-title":"Bioinformatics"},{"key":"2023020202234386100_btv249-B5","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1186\/1471-2164-9-145","article-title":"A generic approach to identify Transcription Factor-specific operator motifs; Inferences for LacI-family mediated regulation in Lactobacillus plantarum WCFS1","volume":"9","author":"Francke","year":"2008","journal-title":"BMC Genomics"},{"key":"2023020202234386100_btv249-B6","doi-asserted-by":"crossref","first-page":"202","DOI":"10.1186\/1471-2164-13-202","article-title":"Comparing thousands of circular genomes using the CGView Comparison Tool","volume":"13","author":"Grant","year":"2012","journal-title":"BMC Genomics"},{"key":"2023020202234386100_btv249-B7","doi-asserted-by":"crossref","first-page":"204","DOI":"10.4056\/sigs.28608","article-title":"GeneWiz browser: an interactive tool for visualizing sequenced chromosomes","volume":"1","author":"Hallin","year":"2009","journal-title":"Standards Genomic Sci."},{"key":"2023020202234386100_btv249-B8","doi-asserted-by":"crossref","first-page":"1812","DOI":"10.1093\/bioinformatics\/bth159","article-title":"Visualization for genomics: the Microbial Genome Viewer","volume":"20","author":"Kerkhoven","year":"2004","journal-title":"Bioinformatics"},{"key":"2023020202234386100_btv249-B9","doi-asserted-by":"crossref","first-page":"1639","DOI":"10.1101\/gr.092759.109","article-title":"Circos: an information aesthetic for comparative genomics","volume":"19","author":"Krzywinski","year":"2009","journal-title":"Genome Res."},{"key":"2023020202234386100_btv249-B10","doi-asserted-by":"crossref","first-page":"401","DOI":"10.1186\/1471-2164-13-401","article-title":"High-and low-affinity CRE boxes for CcpA binding in Bacillus subtilis revealed by genome-wide analysis","volume":"13","author":"Marciniak","year":"2012","journal-title":"BMC Genomics"},{"key":"2023020202234386100_btv249-B11","doi-asserted-by":"crossref","first-page":"D241","DOI":"10.1093\/nar\/gkq1093","article-title":"PSORTdb\u2014an expanded, auto-updated, user-friendly protein subcellular localization database for Bacteria and Archaea","volume":"39","author":"Nancy","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"2023020202234386100_btv249-B12","doi-asserted-by":"crossref","first-page":"209","DOI":"10.1186\/1471-2164-14-209","article-title":"MGcV: the microbial genomic context viewer for comparative genome analysis","volume":"14","author":"Overmars","year":"2013","journal-title":"BMC Genomics"},{"key":"2023020202234386100_btv249-B13","doi-asserted-by":"crossref","first-page":"D130","DOI":"10.1093\/nar\/gkr1079","article-title":"NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy","volume":"40","author":"Pruitt","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"2023020202234386100_btv249-B14","doi-asserted-by":"crossref","first-page":"537","DOI":"10.1093\/bioinformatics\/bti054","article-title":"Circular genome visualization and exploration using CGView","volume":"21","author":"Stothard","year":"2005","journal-title":"Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/31\/17\/2867\/49035269\/bioinformatics_31_17_2867.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/31\/17\/2867\/49035269\/bioinformatics_31_17_2867.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T03:47:46Z","timestamp":1675309666000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/31\/17\/2867\/183091"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015,4,24]]},"references-count":14,"journal-issue":{"issue":"17","published-print":{"date-parts":[[2015,9,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btv249","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2015,9,1]]},"published":{"date-parts":[[2015,4,24]]}}}