{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,27]],"date-time":"2026-03-27T02:16:44Z","timestamp":1774577804184,"version":"3.50.1"},"reference-count":9,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2016,5,6]],"date-time":"2016-05-06T00:00:00Z","timestamp":1462492800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2016,5,6]],"date-time":"2016-05-06T00:00:00Z","timestamp":1462492800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/501100006488","name":"Institut National de la Recherche Agronomique","doi-asserted-by":"publisher","award":["PhD"],"award-info":[{"award-number":["PhD"]}],"id":[{"id":"10.13039\/501100006488","id-type":"DOI","asserted-by":"publisher"}]},{"name":"R\u00e9gion Centre Val de Loire","award":["AviGeS"],"award-info":[{"award-number":["AviGeS"]}]},{"DOI":"10.13039\/501100004794","name":"Centre National de la Recherche Scientifique","doi-asserted-by":"publisher","award":["GDR 3546"],"award-info":[{"award-number":["GDR 3546"]}],"id":[{"id":"10.13039\/501100004794","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"abstract":"<jats:title>Abstract<\/jats:title><jats:sec>\n                <jats:title>Background<\/jats:title>\n                <jats:p>Several tools are available for visualizing genomic data. Some, such as Gbrowse and Jbrowse, are very efficient for small genomic regions, but they are not suitable for entire genomes. Others, like Phenogram and CViT, can be used to visualise whole genomes, but are not designed to display very dense genomic features (eg: interspersed repeats). We have therefore developed DensityMap, a lightweight Perl program that can display the densities of several features (genes, ncRNA, cpg, etc.) along chromosomes on the scale of the whole genome. A critical advantage of DensityMap is that it uses GFF annotation files directly to compute the densities of features without needing additional information from the user. The resulting picture is readily configurable, and the colour scales used can be customized for a best fit to the data plotted.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>DensityMap runs on Linux architecture with few requirements so that users can easily and quickly visualize the distributions and densities of genomic features for an entire genome. The input is GFF3-formated data representing chromosomes (linkage groups or pseudomolecules) and sets of features which are used to calculate representations in density maps. In practise, DensityMap uses a tilling window to compute the density of one or more features and the number of bases covered by these features along chromosomes. The densities are represented by colour scales that can be customized to highlight critical points. DensityMap can compare the distributions of features; it calculates several chromosomal density maps in a single image, each of which describes a different genomic feature. It can also use the genome nucleotide sequence to compute and plot a density map of the GC content along chromosomes.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusions<\/jats:title>\n                <jats:p>DensityMap is a compact, easily-used tool for displaying the distribution and density of all types of genomic features within a genome. It is flexible enough to visualize the densities of several types of features in a single representation. The images produced are readily configurable and their SVG format ensures that they can be edited.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s12859-016-1055-0","type":"journal-article","created":{"date-parts":[[2016,5,6]],"date-time":"2016-05-06T09:21:40Z","timestamp":1462526500000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":16,"title":["DensityMap: a genome viewer for illustrating the densities of features"],"prefix":"10.1186","volume":"17","author":[{"given":"S\u00e9bastien","family":"Guizard","sequence":"first","affiliation":[]},{"given":"Beno\u00eet","family":"Pi\u00e9gu","sequence":"additional","affiliation":[]},{"given":"Yves","family":"Bigot","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2016,5,6]]},"reference":[{"key":"1055_CR1","doi-asserted-by":"publisher","first-page":"333","DOI":"10.2144\/000113134","volume":"46","author":"J Batley","year":"2009","unstructured":"Batley J, Edwards D. Genome sequence data: Management, storage, and visualization. Biotechniques. 2009;46:333\u20135.","journal-title":"Biotechniques"},{"key":"1055_CR2","doi-asserted-by":"publisher","first-page":"996","DOI":"10.1101\/gr.229102. Article published online before print in May 2002","volume":"12","author":"WJ Kent","year":"2002","unstructured":"Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, et al. The Human Genome Browser at UCSC. Genome Res. 2002;12:996\u20131006.","journal-title":"Genome Res"},{"key":"1055_CR3","doi-asserted-by":"publisher","first-page":"131","DOI":"10.1093\/bib\/bbs029","volume":"14","author":"J Wang","year":"2013","unstructured":"Wang J, Kong L, Gao G, Luo J. A brief introduction to web-based genome browsers. Brief Bioinformatics. 2013;14:131\u201343.","journal-title":"Brief Bioinformatics"},{"key":"1055_CR4","doi-asserted-by":"publisher","first-page":"R93","DOI":"10.1186\/gb-2013-14-8-r93","volume":"14","author":"E Lee","year":"2013","unstructured":"Lee E, Helt G, Reese JT, Munoz-Torres MC, Childers CP, et al. Web Apollo: a web-based genomic annotation editing platform. Genome Biol. 2013;14:R93.","journal-title":"Genome Biol"},{"key":"1055_CR5","doi-asserted-by":"publisher","first-page":"1639","DOI":"10.1101\/gr.092759.109","volume":"19","author":"M Krzywinski","year":"2009","unstructured":"Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, et al. Circos: An information aesthetic for comparative genomics. Genome Res. 2009;19:1639\u201345.","journal-title":"Genome Res"},{"key":"1055_CR6","doi-asserted-by":"publisher","first-page":"1463","DOI":"10.1093\/bioinformatics\/btu842","volume":"31","author":"J An","year":"2015","unstructured":"An J, Lai J, Sajjanhar A, Batra J, Wang C, et al. J-Circos: an interactive Circos plotter. Bioinformatics. 2015;31:1463\u20135.","journal-title":"Bioinformatics"},{"key":"1055_CR7","doi-asserted-by":"publisher","first-page":"1030","DOI":"10.1111\/tpj.12366","volume":"76","author":"C Pont","year":"2013","unstructured":"Pont C, Murat F, Guizard S, Flores R, Foucrier S, et al. Wheat syntenome unveils new evidences of contrasted evolutionary plasticity between paleo- and neoduplicated subgenomes. Plant J. 2013;76:1030\u201344.","journal-title":"Plant J"},{"key":"1055_CR8","doi-asserted-by":"publisher","first-page":"18","DOI":"10.1186\/1756-0381-6-18","volume":"6","author":"D Wolfe","year":"2013","unstructured":"Wolfe D, Dudek S, Ritchie MD, Pendergrass S. Visualizing genomic information across chromosomes with PhenoGram. BioData Mining. 2013;6:18.","journal-title":"BioData Mining"},{"key":"1055_CR9","first-page":"373875","volume":"2011","author":"EKS Cannon","year":"2011","unstructured":"Cannon EKS, Cannon SB. Chromosome visualization tool: a whole genome viewer. International J plant genom. 2011;2011:373875.","journal-title":"International J plant genom"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-016-1055-0.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s12859-016-1055-0\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-016-1055-0","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-016-1055-0.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,2,1]],"date-time":"2024-02-01T18:23:54Z","timestamp":1706811834000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-016-1055-0"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016,5,6]]},"references-count":9,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2016,12]]}},"alternative-id":["1055"],"URL":"https:\/\/doi.org\/10.1186\/s12859-016-1055-0","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2016,5,6]]},"assertion":[{"value":"19 January 2016","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"13 April 2016","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"6 May 2016","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"204"}}