Junker: An Intergenic Explorer for Bacterial Genomes

Genomics, Proteomics and Bioinformatics

Volumn 9, Issue 4-5, 2011, Pages 179-182

  Sridhar, Jayavel ^a   Sabarinathan, Radhakrishnan ^b   Balan, Shanmugam Siva ^b   Rafi, Ziauddin Ahamed ^a   Gunasekaran, Paramasamy ^a   Sekar, Kanagaraj ^b  

^a MADURAI KAMARAJ UNIVERSITY   (India)

^b INDIAN INSTITUTE OF SCIENCE   (India)

Author keywords

Bacterial genome; Intergenic region; Statistics module; Web server

Indexed keywords

SPACER DNA;

ARTICLE; BACTERIAL GENOME; DENSITY; GENE MAPPING; GENE SEQUENCE; GENOME ANALYSIS; INTERNET; LOCAL GENE DENSITY; MICROPROCESSOR; NONHUMAN; NUCLEOTIDE SEQUENCE; WEB SERVER;

CHROMOSOME MAPPING; DNA, INTERGENIC; GENOME, BACTERIAL; GENOMICS; INTERNET; SOFTWARE;

EID: 84255170497     PISSN: 16720229     EISSN: 22103244     Source Type: Journal    
DOI: 10.1016/S1672-0229(11)60021-1     Document Type: Article

References (20)

1. Wassarman K.M., et al. Identification of novel small RNAs using comparative genomics and microarrays. Genes Dev. 2001, 15:1637-1651.
2. Hershberg R., et al. A survey of small-RNA encoding genes in Escherichia coli. Nucleic Acids Res 2003, 31:1813-1820.
3. Siguier P., et al. Insertion sequences in prokaryotic genomes. Curr. Opin. Microbiol. 2006, 9:526-531.
4. Doublet B., et al. Secondary chromosomal attachment site and tandem integration of the mobilizable Salmonella genomic island 1. PLoS One 2008, 3:e2060.
5. Sharples G.J., Lloyd R.G. A novel repeated DNA sequence located in the intergenic regions of bacterial chromosomes. Nucleic Acids Res. 1990, 18:6503-6508.
6. Fu L.M., Shinnick T.M. 2007. Genome-wide analysis of intergenic regions of Mycobacterium tuberculosis H37Rv using Affymetrix GeneChips. EURASIP J. Bioinform. Syst. Biol. 2007, 23054.
7. Blattner F.R., et al. The complete genome sequence of Escherichia coli K-12. Science 1997, 277:1453-1462.
8. Taft R.J., et al. The relationship between non-protein-coding DNA and eukaryotic complexity. Bioessays 2007, 29:288-299.
9. Ray W.C., Daniels C.J. PACRAT: a database and analysis system for archaeal and bacterial intergenic sequence features. Nucleic Acids Res. 2003, 31:109-113.
10. Oberto J. BAGET: a web server for the effortless retrieval of prokaryotic gene context and sequence. Bioinformatics 2008, 24:424-425.
11. Haas B.J., et al. Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans. Nature 2009, 461:393-398.
12. Chiapello H., et al. MOSAIC: an online database dedicated to the comparative genomics of bacterial strains at the intra-species level. BMC Bioinformatics 2008, 9:498.
13. Banos R.C., et al. Differential regulation of horizontally acquired and core genome genes by the bacterial modulator H-NS. PLoS Genet. 2009, 5:e1000513.
14. Borodovsky M., McIninch J. GeneMark: parallel gene recognition for both DNA strands. Comput. Chem. 1993, 17:123-133.
15. Delcher A.L., et al. Improved microbial gene identification with GLIMMER. Nucleic Acids Res. 1999, 27:4636-4641.
16. Hyatt D., et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 2010, 11:119.
17. Banerjee N., et al. An algorithm to find all identical internal sequence repeats. Curr. Sci. 2008, 95:188-195.
18. Rice P., et al. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000, 16:276-277.
19. Toh H., et al. Massive genome erosion and functional adaptations provide insights into the symbiotic lifestyle of Sodalis glossinidius in the tsetse host. Genome Res. 2006, 16:149-156.
20. Cho N.H., et al. The Orientia tsutsugamushi genome reveals massive proliferation of conjugative type IV secretion system and host-cell interaction genes. Proc. Natl. Acad. Sci. USA 2007, 104:7981-7986.