SeqWord Gene Island Sniffer: a Program to Study the Lateral Genetic Exchange among Bacteria

Authors: Bezuidt O., Lima-Mendez G., Reva O. N.

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

Digital Object Identifier (DOI): doi.org/10.5281/zenodo.1071430

References:

[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.