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Allows for the computational identification of transposon insertion sites in known bacterial genome sequences after transposon mutagenesis experiments. The used approach is based on the observation that restriction endonucleases digestions of bacterial DNA yields unique pattern of DNA fragments with defined sizes. Transposon insertion changes the size of the hosting DNA fragment by a known number of base pairs. The exact sizes of this fragment can be determinate by Southern blot hybridization and identified with subsequent computational analysis.

Software type:
Package
Interface:
Command line interface
Restrictions to use:
None
Operating system:
Unix/Linux, Mac OS, Windows
Programming languages:
R
Computer skills:
Advanced
Version:
InFiRe version 2.0
Stability:
Stable
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Interface:
Web user interface
Restrictions to use:
None
Programming languages:
R
Computer skills:
Basic
Version:
InFiRe version 2.0
Stability:
Stable
View all reviews

0 user review

No review has been posted.

View all issues

0 issue

No open issue.

Links

Maintainer

  • Louisa Roselius <l.roselius at tu-bs.de>

Institution(s)

Institute of Microbiology, Technische Universität Braunschweig, Spielmannstrasse 7, 38106 Braunschweig, Germany

Funding source(s)

Deutsche Forschungs-gemeinschaft (DFG, grant SFBTR51); Bundesministerium für Bildung und Forschung (BMBF) medical infection genomics (grant no. 0315831A, 0315833A)

  • (Shevchuk et al., 2012) InFiRe — a novel computational method for the identification of insertion sites in transposon mutagenized bacterial genomes. Bioinformatics.
    PMID: 22155866
  • Eubacteria
  • (Bergman and Quesneville, 2007) Discovering and detecting transposable elements in genome sequences. Briefings in bioinformatics.
    PMID: 17932080
  • (Anisimova et al., 2015) Statistical approaches to detecting and analyzing tandem repeats in genomic sequences. Frontiers in bioengineering and biotechnology.
    PMID: 25853125
  • (Saha et al., 2008) Empirical comparison of ab initio repeat finding programs. Nucleic acids research.
    PMID: 18287116
  • (Lerat, 2010) Identifying repeats and transposable elements in sequenced genomes: how to find your way through the dense forest of programs. Heredity.
    PMID: 19935826
  • (Janicki et al., 2011) Bioinformatics and genomic analysis of transposable elements in eukaryotic genomes. Chromosome research.
    PMID: 21850457

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