{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,21]],"date-time":"2025-02-21T13:35:03Z","timestamp":1740144903325,"version":"3.37.3"},"reference-count":20,"publisher":"Oxford University Press (OUP)","issue":"4-5","license":[{"start":{"date-parts":[[2024,5,10]],"date-time":"2024-05-10T00:00:00Z","timestamp":1715299200000},"content-version":"vor","delay-in-days":4605,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-sa\/3.0\/"}],"funder":[{"DOI":"10.13039\/100007780","name":"Indian Institute of Science","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100007780","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Department of Biotechnology, Government of India"},{"name":"Networking Resource Centre in Biological Sciences"},{"DOI":"10.13039\/501100008228","name":"Madurai Kamaraj University","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100008228","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,10,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>In the past few decades, scientists from all over the world have taken a keen interest in novel functional units such as small regulatory RNAs, small open reading frames, pseudogenes, transposons, integrase binding attB\/attP sites, repeat elements within the bacterial intergenic regions (IGRs) and in the analysis of those \u201cjunk\u201d regions for genomic complexity. Here we have developed a web server, named Junker, to facilitate the in-depth analysis of IGRs for examining their length distribution, four-quadrant plots, GC percentage and repeat details. Upon selection of a particular bacterial genome, the physical genome map is displayed as a multiple loci with options to view any loci of interest in detail. In addition, an IGR statistics module has been created and implemented in the web server to analyze the length distribution of the IGRs and to understand the disordered grouping of IGRs across the genome by generating the four-quadrant plots. The proposed web server is freely available at the URL http:\/\/pranag.physics.iisc.ernet.in\/junker\/.<\/jats:p>","DOI":"10.1016\/s1672-0229(11)60021-1","type":"journal-article","created":{"date-parts":[[2011,12,23]],"date-time":"2011-12-23T20:05:29Z","timestamp":1324670729000},"page":"179-182","source":"Crossref","is-referenced-by-count":10,"title":["Junker: An Intergenic Explorer for Bacterial Genomes"],"prefix":"10.1093","volume":"9","author":[{"given":"Jayavel","family":"Sridhar","sequence":"first","affiliation":[{"name":"Centre of Excellence in Bioinformatics, School of Biotechnology, Madurai Kamaraj University , Madurai, Tamilnadu, 625021 , India"},{"name":"UGC-Networking Resource Centre in Biological Sciences, School of Biological Sciences, Madurai Kamaraj University , Madurai, Tamilnadu, 625021 , India"}]},{"given":"Radhakrishnan","family":"Sabarinathan","sequence":"additional","affiliation":[{"name":"Bioinformatics Centre, Indian Institute of Science , Bangalore, Karnataka, 560012 , India"}]},{"given":"Shanmugam Siva","family":"Balan","sequence":"additional","affiliation":[{"name":"Bioinformatics Centre, Indian Institute of Science , Bangalore, Karnataka, 560012 , India"}]},{"given":"Ziauddin Ahamed","family":"Rafi","sequence":"additional","affiliation":[{"name":"Centre of Excellence in Bioinformatics, School of Biotechnology, Madurai Kamaraj University , Madurai, Tamilnadu, 625021 , India"}]},{"given":"Paramasamy","family":"Gunasekaran","sequence":"additional","affiliation":[{"name":"UGC-Networking Resource Centre in Biological Sciences, School of Biological Sciences, Madurai Kamaraj University , Madurai, Tamilnadu, 625021 , India"}]},{"given":"Kanagaraj","family":"Sekar","sequence":"additional","affiliation":[{"name":"Bioinformatics Centre, Indian Institute of Science , Bangalore, Karnataka, 560012 , India"}]}],"member":"286","published-online":{"date-parts":[[2011,12,23]]},"reference":[{"key":"2024051008285571500_bib1","doi-asserted-by":"crossref","first-page":"1637","DOI":"10.1101\/gad.901001","article-title":"Identification of novel small RNAs using comparative genomics and microarrays","volume":"15","author":"Wassarman","year":"2001","journal-title":"Genes Dev."},{"key":"2024051008285571500_bib2","doi-asserted-by":"crossref","first-page":"1813","DOI":"10.1093\/nar\/gkg297","article-title":"A survey of small-RNA encoding genes in Escherichia coli","volume":"31","author":"Hershberg","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"2024051008285571500_bib3","doi-asserted-by":"crossref","first-page":"526","DOI":"10.1016\/j.mib.2006.08.005","article-title":"Insertion sequences in prokaryotic genomes","volume":"9","author":"Siguier","year":"2006","journal-title":"Curr. 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