title: InFiRe -- a novel computational method for the identification of insertion sites in transposon mutagenized bacterial genomes.
abstract: BACKGROUND
  InFiRe, Insertion Finder via Restriction digest, is a novel software tool that allows for the computational identification of transposon insertion sites in known bacterial genome sequences after transposon mutagenesis experiments. The approach is based on the fact that restriction endonuclease digestions of bacterial DNA yield a 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 size of this fragment can be determined by Southern blot hybridization. Subsequently, the position of insertion can be identified with computational analysis. The outlined method provides a solid basis for the establishment of a new high-throughput technology.
  
  
  METHODS
  The software is freely available on our web server at www.infire.tu-bs.de. The algorithm was implemented in the statistical programming language R. For the most flexible use, InFiRe is provided in two different versions. A web interface offers the convenient use in a web browser. In addition, the software and source code is freely available for download as R-packages on our website.
  
  
  BACKGROUND
  m.steinert@tu-bs.de
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Institute of Microbiology, Technische Universität Braunschweig, Spielmannstrasse 7, 38106 Braunschweig, Germany.
authors.forename: Olga
authors.initials: O
authors.lastname: Shevchuk
authors.forename: Louisa
authors.initials: L
authors.lastname: Roselius
authors.forename: Gabriele
authors.initials: G
authors.lastname: Günther
authors.forename: Johannes
authors.initials: J
authors.lastname: Klein
authors.forename: Dieter
authors.initials: D
authors.lastname: Jahn
authors.forename: Michael
authors.initials: M
authors.lastname: Steinert
authors.forename: Richard
authors.initials: R
authors.lastname: Münch
mesh_terms: D000465:Algorithms; D004251:DNA Transposable Elements; D004269:DNA, Bacterial / Q000235:genetics; D016680:Genome, Bacterial; D020407:Internet; D016952:Legionella pneumophila / Q000235:genetics; D016254:Mutagenesis, Insertional; D012984:Software
chemical_list: D004251:DNA Transposable Elements; D004269:DNA, Bacterial