title: Junker: an intergenic explorer for bacterial genomes.
abstract: 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 "junk" 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/.
authors.affiliation: Centre of Excellence in Bioinformatics, School of Biotechnology, Madurai Kamaraj University, Madurai 625021, Tamilnadu, India.
authors.forename: Jayavel
authors.initials: J
authors.lastname: Sridhar
authors.forename: Radhakrishnan
authors.initials: R
authors.lastname: Sabarinathan
authors.forename: Shanmugam Siva
authors.initials: SS
authors.lastname: Balan
authors.forename: Ziauddin Ahamed
authors.initials: ZA
authors.lastname: Rafi
authors.forename: Paramasamy
authors.initials: P
authors.lastname: Gunasekaran
authors.forename: Kanagaraj
authors.initials: K
authors.lastname: Sekar
mesh_terms: D002874:Chromosome Mapping; D021901:DNA, Intergenic / Q000235:genetics*; D016680:Genome, Bacterial; D023281:Genomics / Q000379:methods*; D020407:Internet; D012984:Software
chemical_list: D021901:DNA, Intergenic