{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,17]],"date-time":"2026-04-17T17:56:14Z","timestamp":1776448574130,"version":"3.51.2"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"17","license":[{"start":{"date-parts":[[2018,4,5]],"date-time":"2018-04-05T00:00:00Z","timestamp":1522886400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Genome plotting is performed using a wide range of visualizations tools each with emphasis on a different informative dimension of the genome. These tools can provide a deeper insight into the genomic structure of the organism.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Here, we announce a new visualization tool that is specifically designed for chloroplast genomes. It allows the users to depict the genetic architecture of up to ten chloroplast genomes in the vicinity of the sites connecting the inverted repeats to the short and long single copy regions. The software and its dependent libraries are fully coded in R and the reflected plot is scaled up to realistic size of nucleotide base pairs in the vicinity of the junction sites. We introduce a website for easier use of the program and R source code of the software to be used in case of preferences to be changed and integrated into personal pipelines. The input of the program is an annotation GenBank (.gb) file, the accession or GI number of the sequence or a DOGMA output file. The software was tested using over a 100 embryophyte chloroplast genomes and in all cases a reliable output was obtained.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Source codes and the online suit available at https:\/\/irscope.shinyapps.io\/irapp\/ or https:\/\/github.com\/Limpfrog\/irscope.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty220","type":"journal-article","created":{"date-parts":[[2018,4,4]],"date-time":"2018-04-04T19:12:36Z","timestamp":1522869156000},"page":"3030-3031","source":"Crossref","is-referenced-by-count":910,"title":["IRscope: an online program to visualize the junction sites of chloroplast genomes"],"prefix":"10.1093","volume":"34","author":[{"given":"Ali","family":"Amiryousefi","sequence":"first","affiliation":[{"name":"Organismal Evolutionary Biology Research Program, Faculty of Biology and Environmental Sciences, Viikki Plant Science Centre"}]},{"given":"Jaakko","family":"Hyv\u00f6nen","sequence":"additional","affiliation":[{"name":"Organismal Evolutionary Biology Research Program, Faculty of Biology and Environmental Sciences, Viikki Plant Science Centre"},{"name":"Finnish Museum of Natural History, University of Helsinki, FI-00014 Helsinki, Finland"}]},{"given":"Peter","family":"Poczai","sequence":"additional","affiliation":[{"name":"Finnish Museum of Natural History, University of Helsinki, FI-00014 Helsinki, Finland"}]}],"member":"286","published-online":{"date-parts":[[2018,4,5]]},"reference":[{"key":"2023061313384203900_bty220-B1","doi-asserted-by":"crossref","first-page":"W273","DOI":"10.1093\/nar\/gkh458","article-title":"VISTA: computational tools for comparative genomics","volume":"32","author":"Frazer","year":"2004","journal-title":"Nucleic Acids Res"},{"key":"2023061313384203900_bty220-B2","doi-asserted-by":"crossref","first-page":"144","DOI":"10.1016\/0005-2787(76)90338-5","article-title":"Physical studies on the size and structure of the covalently closed circular chloroplast DNA from higher plants","volume":"447","author":"Kolodner","year":"1976","journal-title":"Biochim. Biophys. Acta"},{"key":"2023061313384203900_bty220-B3","doi-asserted-by":"crossref","first-page":"189","DOI":"10.1007\/s11427-012-4430-8","article-title":"Complete chloroplast genome sequence of Magnolia grandiflora and comparative analysis with related species","volume":"56","author":"Li","year":"2013","journal-title":"Sci. China. Life Sci"},{"key":"2023061313384203900_bty220-B4","doi-asserted-by":"crossref","first-page":"267","DOI":"10.1007\/s00294-007-0161-y","article-title":"OrganellarGenomeDRAW (OGDRAW)\u2014a tool for the easy generation of high-quality custom graphical maps of plastid and mitochondrial genomes","volume":"52","author":"Lohse","year":"2007","journal-title":"Curr. Genet"},{"key":"2023061313384203900_bty220-B5","doi-asserted-by":"crossref","first-page":"661","DOI":"10.1111\/j.1365-313X.2007.03326.x","article-title":"How to usefully compare homologous plant genes and chromosomes as DNA sequences","volume":"53","author":"Lyons","year":"2008","journal-title":"Plant J"},{"key":"2023061313384203900_bty220-B6","doi-asserted-by":"crossref","first-page":"953","DOI":"10.1016\/j.jmb.2003.11.020","article-title":"Most chloroplast DNA of maze seedlings in linear molecules with defined ends and branched forms","volume":"335","author":"Oldenburg","year":"2004","journal-title":"J. Mol. Biol"},{"key":"2023061313384203900_bty220-B7","doi-asserted-by":"crossref","first-page":"92","DOI":"10.1038\/301092a0","article-title":"Chloroplast DNA exists in two orientations","volume":"301","author":"Palmer","year":"1983","journal-title":"Nature"},{"key":"2023061313384203900_bty220-B9","doi-asserted-by":"crossref","first-page":"1751","DOI":"10.3732\/ajb.1500299","article-title":"Sources of inversion variation in the small single copy (SSC) region of chloroplast genomes","volume":"102","author":"Walker","year":"2015","journal-title":"Am. J. Botany"},{"key":"2023061313384203900_bty220-B10","doi-asserted-by":"crossref","first-page":"3252","DOI":"10.1093\/bioinformatics\/bth352","article-title":"Automatic annotation of organellar genomes with DOGMA","volume":"20","author":"Wyman","year":"2004","journal-title":"Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/17\/3030\/50581985\/bioinformatics_34_17_3030.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/17\/3030\/50581985\/bioinformatics_34_17_3030.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,13]],"date-time":"2023-06-13T13:39:59Z","timestamp":1686663599000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/34\/17\/3030\/4961430"}},"subtitle":[],"editor":[{"given":"John","family":"Hancock","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2018,4,5]]},"references-count":9,"journal-issue":{"issue":"17","published-print":{"date-parts":[[2018,9,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bty220","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2018,9,1]]},"published":{"date-parts":[[2018,4,5]]}}}