Junker: An Intergenic Explorer for Bacterial Genomes

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/.

[1]  G. Storz,et al.  Identification of novel small RNAs using comparative genomics and microarrays. , 2001, Genes & development.

[2]  Christophe Caron,et al.  MOSAIC: an online database dedicated to the comparative genomics of bacterial strains at the intra-species level , 2008, BMC Bioinformatics.

[3]  M. Pons,et al.  Differential Regulation of Horizontally Acquired and Core Genome Genes by the Bacterial Modulator H-NS , 2009, PLoS genetics.

[4]  Li M. Fu,et al.  Genome-Wide Analysis of Intergenic Regions of Mycobacterium tuberculosis H37Rv Using Affymetrix GeneChips , 2007, EURASIP J. Bioinform. Syst. Biol..

[5]  S. Salzberg,et al.  Improved microbial gene identification with GLIMMER. , 1999, Nucleic acids research.

[6]  Jacques Oberto.  BAGET: a web server for the effortless retrieval of prokaryotic gene context and sequence , 2008, Bioinform..

[7]  K. Sekar,et al.  An algorithm to find all identical internal sequence repeats , 2008 .

[8]  William C. Ray,et al.  PACRAT: a database and analysis system for archaeal and bacterial intergenic sequence features , 2003, Nucleic Acids Res..

[9]  Mark Borodovsky,et al.  GENMARK: Parallel Gene Recognition for Both DNA Strands , 1993, Comput. Chem..

[10]  R. G. Lloyd,et al.  A novel repeated DNA sequence located in the intergenic regions of bacterial chromosomes. , 1990, Nucleic acids research.

[11]  Miriam L. Land,et al.  Trace: Tennessee Research and Creative Exchange Prodigal: Prokaryotic Gene Recognition and Translation Initiation Site Identification Recommended Citation Prodigal: Prokaryotic Gene Recognition and Translation Initiation Site Identification , 2022 .

[12]  N. W. Davis,et al.  The complete genome sequence of Escherichia coli K-12. , 1997, Science.

[13]  I. Longden,et al.  EMBOSS: the European Molecular Biology Open Software Suite. , 2000, Trends in genetics : TIG.

[14]  M. Mulvey,et al.  Secondary Chromosomal Attachment Site and Tandem Integration of the Mobilizable Salmonella Genomic Island 1 , 2008, PloS one.

[15]  Patricia Siguier,et al.  Insertion sequences in prokaryotic genomes. , 2006, Current opinion in microbiology.

[16]  Jonathan D. G. Jones,et al.  Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans , 2009, Nature.

[17]  H. Margalit,et al.  A survey of small RNA-encoding genes in Escherichia coli. , 2003, Nucleic acids research.

[18]  Jihun Kim,et al.  The Orientia tsutsugamushi genome reveals massive proliferation of conjugative type IV secretion system and host–cell interaction genes , 2007, Proceedings of the National Academy of Sciences.

[19]  J. Mattick,et al.  The relationship between non-protein-coding DNA and eukaryotic complexity. , 2007, BioEssays : news and reviews in molecular, cellular and developmental biology.

[20]  Masahira Hattori,et al.  Massive genome erosion and functional adaptations provide insights into the symbiotic lifestyle of Sodalis glossinidius in the tsetse host. , 2005, Genome research.