SeqWord Gene Island Sniffer: a Program to Study the Lateral Genetic Exchange among Bacteria
SeqWord Gene Island Sniffer, a new program for
the identification of mobile genetic elements in sequences of bacterial chromosomes is presented. This program is based on the
analysis of oligonucleotide usage variations in DNA sequences. 3,518 mobile genetic elements were identified in 637 bacterial
genomes and further analyzed by sequence similarity and the
functionality of encoded proteins. The results of this study are stored in an open database http://anjie.bi.up.ac.za/geidb/geidbhome.
php). The developed computer program and the database provide the information valuable for further investigation of the
distribution of mobile genetic elements and virulence factors among bacteria. The program is available for download at www.bi.up.ac.za/SeqWord/sniffer/index.html.
[1] M. Juhas, J. R. van der Meer, M. Gaillard, R. M. Harding, D. W. Hood
and D. W. Hood. "Genomic islands: tools of bacterial horizontal gene
transfer and evolution," FEMS Microbiol Rev, 2009, 33, pp. 376-393.
[2] U. Dobrindt, B. Hochhut, U. Hentschel and J. Hacker. "Genomic islands
in pathogenic and environmental organisms," Nat Rev Microbiol, 2004,
2, pp. 414-424.
[3] C. Dufraigne, B. Fertil, S. Lespinats, A. Giron and P. Deschavanne.
"Detection and characterization of horizontal transfers in prokaryotes
using genomic signatures," NAR, 2005, 33.
[4] J. Li and K. Sayood. "A genome signature based on Markov modeling,"
in Proc IEEE Eng Med Biol Soc, 2005, pp. 2832-2835.
[5] O. N. Reva and B. T├╝mmler. "Differentiation of regions with atypical
oligonucleotide composition in bacterial genomes," BMC
Bioinformatics, 2005, 6, pp. 251.
[6] S. Karlin. "Global dinucleotide signatures and analysis of genomic
heterogeneity," Curr Opinion Microbiol, 1998, 1, pp. 598-610.
[7] S. Karlin, J. Mrázek and A. M. Campbell. "Compositional biases of
bacterial genomes and evolutionary implications," J Bacteriol, 1997,
179, pp. 3899-3913.
[8] P. A. Noble, R. W. Citek and O. A. Oqunseitan. "Tetranucleotide
frequencies in microbial genomes," Electrophoresis, 1998, 19, 528-535.
[9] D. T. Pride, R. J. Meinersmann, T. M. Wassenaar and M. J. Blaser.
"Evolutionary implications of microbial genome tetranucleotide
frequency biases," Genome Res, 2003, 13, pp. 145-158.
[10] O. N. Reva and B. T├╝mmler. "Global features of sequences of bacterial
chromosomes, plasmids and phages revealed by analysis of
oligonucleotide usage patterns," BMC Bioinformatics, 2004, 5, pp. 90.
[11] H. Ganesan, A. S. Rakitianskaia, C. F. Davenport, B. T├╝mmler and O. Reva. "The SeqWord genome browser: an online tool for the identification and visualization of atypical regions of bacterial
genomes," BMC Bioinformatics, 2008, 9, pp. 333.
[12] G. Lima-Mendez, J. van Helden, A. Toussaint and R. Leplae. "Prophinder: a computational tool for prophage prediction in prokaryotic
genomes," Bioinformatics, 2008, 24, pp. 863-865.
[13] W. S. Jermyn and E. F. Boyd. "Molecular evolution of Vibrio
pathogenicity island-2 (VPI-2): mosaic structure among Vibrio cholera
and Vibrio mimicus natural isolates," Microbiology, 2005, 151, pp. 311-322.
[14] K. Jann and B. Jann. "Assembly of cellular surface structures," in Biology of the Prokaryotes, ed. J. W. Lengeler, G. Drews and H. G.
Schlegel, Blackwell Science, Oxford, 1999, pp. 555-570.
[15] M. Kanehisa. "From genomics to chemical genomics: new developments
in KEGG," NAR, 2006, 34, pp. D354-D357.
[16] C. F. Snook, P. A. Tipton and L. J. Beamer. "Crystal structure of GDPmannose
dehydrogenase: a key enzyme of alginate biosynthesis in
P. aeruginosa," Biochemistry, 2003, 42, 4658-4668.
[17] G. Lima-Mendez, J. van Helden, A. Toussaint and R. Leplae. "Reticulate
representation of evolutionary and functional relationships between phage genomes," Mol Biol Evol, 2008, 25, pp. 762-777.
[1] M. Juhas, J. R. van der Meer, M. Gaillard, R. M. Harding, D. W. Hood
and D. W. Hood. "Genomic islands: tools of bacterial horizontal gene
transfer and evolution," FEMS Microbiol Rev, 2009, 33, pp. 376-393.
[2] U. Dobrindt, B. Hochhut, U. Hentschel and J. Hacker. "Genomic islands
in pathogenic and environmental organisms," Nat Rev Microbiol, 2004,
2, pp. 414-424.
[3] C. Dufraigne, B. Fertil, S. Lespinats, A. Giron and P. Deschavanne.
"Detection and characterization of horizontal transfers in prokaryotes
using genomic signatures," NAR, 2005, 33.
[4] J. Li and K. Sayood. "A genome signature based on Markov modeling,"
in Proc IEEE Eng Med Biol Soc, 2005, pp. 2832-2835.
[5] O. N. Reva and B. T├╝mmler. "Differentiation of regions with atypical
oligonucleotide composition in bacterial genomes," BMC
Bioinformatics, 2005, 6, pp. 251.
[6] S. Karlin. "Global dinucleotide signatures and analysis of genomic
heterogeneity," Curr Opinion Microbiol, 1998, 1, pp. 598-610.
[7] S. Karlin, J. Mrázek and A. M. Campbell. "Compositional biases of
bacterial genomes and evolutionary implications," J Bacteriol, 1997,
179, pp. 3899-3913.
[8] P. A. Noble, R. W. Citek and O. A. Oqunseitan. "Tetranucleotide
frequencies in microbial genomes," Electrophoresis, 1998, 19, 528-535.
[9] D. T. Pride, R. J. Meinersmann, T. M. Wassenaar and M. J. Blaser.
"Evolutionary implications of microbial genome tetranucleotide
frequency biases," Genome Res, 2003, 13, pp. 145-158.
[10] O. N. Reva and B. T├╝mmler. "Global features of sequences of bacterial
chromosomes, plasmids and phages revealed by analysis of
oligonucleotide usage patterns," BMC Bioinformatics, 2004, 5, pp. 90.
[11] H. Ganesan, A. S. Rakitianskaia, C. F. Davenport, B. T├╝mmler and O. Reva. "The SeqWord genome browser: an online tool for the identification and visualization of atypical regions of bacterial
genomes," BMC Bioinformatics, 2008, 9, pp. 333.
[12] G. Lima-Mendez, J. van Helden, A. Toussaint and R. Leplae. "Prophinder: a computational tool for prophage prediction in prokaryotic
genomes," Bioinformatics, 2008, 24, pp. 863-865.
[13] W. S. Jermyn and E. F. Boyd. "Molecular evolution of Vibrio
pathogenicity island-2 (VPI-2): mosaic structure among Vibrio cholera
and Vibrio mimicus natural isolates," Microbiology, 2005, 151, pp. 311-322.
[14] K. Jann and B. Jann. "Assembly of cellular surface structures," in Biology of the Prokaryotes, ed. J. W. Lengeler, G. Drews and H. G.
Schlegel, Blackwell Science, Oxford, 1999, pp. 555-570.
[15] M. Kanehisa. "From genomics to chemical genomics: new developments
in KEGG," NAR, 2006, 34, pp. D354-D357.
[16] C. F. Snook, P. A. Tipton and L. J. Beamer. "Crystal structure of GDPmannose
dehydrogenase: a key enzyme of alginate biosynthesis in
P. aeruginosa," Biochemistry, 2003, 42, 4658-4668.
[17] G. Lima-Mendez, J. van Helden, A. Toussaint and R. Leplae. "Reticulate
representation of evolutionary and functional relationships between phage genomes," Mol Biol Evol, 2008, 25, pp. 762-777.
@article{"International Journal of Information, Control and Computer Sciences:57801", author = "Bezuidt O. and Lima-Mendez G. and Reva O. N.", title = "SeqWord Gene Island Sniffer: a Program to Study the Lateral Genetic Exchange among Bacteria", abstract = "SeqWord Gene Island Sniffer, a new program for
the identification of mobile genetic elements in sequences of bacterial chromosomes is presented. This program is based on the
analysis of oligonucleotide usage variations in DNA sequences. 3,518 mobile genetic elements were identified in 637 bacterial
genomes and further analyzed by sequence similarity and the
functionality of encoded proteins. The results of this study are stored in an open database http://anjie.bi.up.ac.za/geidb/geidbhome.
php). The developed computer program and the database provide the information valuable for further investigation of the
distribution of mobile genetic elements and virulence factors among bacteria. The program is available for download at www.bi.up.ac.za/SeqWord/sniffer/index.html.", keywords = "mobile genetic elements, virulence, bacterial genomes", volume = "3", number = "10", pages = "2411-6", }
