Abstract
We describe here the use of the ISfinder database and its associated software. ISfinder was conceived initially as a comprehensive database for prokaryotic insertion sequences (ISs). It now includes software for visualising complete and partial IS copies in whole genomes (ISbrowser) and for high-quality genome annotation (Insertion Sequence Semi-automatic Genome Annotation).
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References
Siguier P, et al. (2006) ISfinder: the reference centre for bacterial insertion sequences. Nucleic Acids Res 34:D32–36
Dobrindt U, et al. (2004) Genomic islands in pathogenic and environmental microorganisms. Nat Rev Microbiol 2:414–424
Binnewies TT, et al. (2006) Ten years of bacterial genome sequencing: comparative-genomics-based discoveries. Funct Integr Genomics 6:165–185
Altschul SF, et al. (1990) Basic local alignment search tool. J Mol Biol 215:403–410
Hickman AB, Chandler M, Dyda F (2010) Integrating prokaryotes and eukaryotes: DNA transposases in light of structure. Crit Rev Biochem Mol Biol 45:50–69
Chandler M, Mahillon J (2002) Insertion sequences revisited. In Craig NL, Craigie R, Gellert M, Lambowitz A (eds) Mobile DNA. ASM press, Washington DC
Siguier P, Gagnevin L, Chandler M (2009) The new IS1595 family, its relation to IS1 and the frontier between insertion sequences and transposons. Res Microbiol 160:232–241
Mahillon J, Chandler M (1998) Insertion sequences. Microbiol Mol Biol Rev 62:725–774
Campbell A, Berg DE, Botstein D, et al. (1979). Nomenclature of transposable elements in prokaryotes. Gene 5:197–206
Kichenaradja P, et al. (2010). ISbrowser: an extension of ISfinder for visualizing insertion sequences in prokaryotic genomes. Nucleic Acids Res 38:D62-68
Stothard P, Wishart DS (2005). Circular genome visualization and exploration using CGView. Bioinformatics 21:537–539
Varani AM, et al. (2011) ISsaga is an ensemble of web-based methods for high throughput identification and semi-automatic annotation of insertion sequences in prokaryotic genomes. Genome Biol 12:R30
Curcio MJ, Derbyshire KM (2003). The outs and ins of transposition: from Mu to Kangaroo. Nat Rev Mol Cell Biol 4:865–877
Aziz RK, Breitbart M, Edwards RA (2010). Transposases are the most abundant, most ubiquitous genes in nature. Nucleic Acids Res 38:4207–4217
Zerillo MM, et al. (2008) Characterization of new IS elements and studies of their dispersion in two subspecies of Leifsonia xyli. BMC Microbiol 8:127
Burrus V, Waldor MK (2004) Shaping bacterial genomes with integrative and conjugative elements. Res Microbiol 155:376–386
Mazel D (2006) Integrons: agents of bacterial evolution. Nat Rev Microbiol 4:608–620
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Siguier, P., Varani, A., Perochon, J., Chandler, M. (2012). Exploring Bacterial Insertion Sequences with ISfinder: Objectives, Uses, and Future Developments. In: Bigot, Y. (eds) Mobile Genetic Elements. Methods in Molecular Biology, vol 859. Humana Press. https://doi.org/10.1007/978-1-61779-603-6_5
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DOI: https://doi.org/10.1007/978-1-61779-603-6_5
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