title: ACID: annotation of cassette and integron data.
abstract: BACKGROUND
  Although integrons and their associated gene cassettes are present in ~10% of bacteria and can represent up to 3% of the genome in which they are found, very few have been properly identified and annotated in public databases. These genetic elements have been overlooked in comparison to other vectors that facilitate lateral gene transfer between microorganisms.
  
  
  METHODS
  By automating the identification of integron integrase genes and of the non-coding cassette-associated attC recombination sites, we were able to assemble a database containing all publicly available sequence information regarding these genetic elements. Specialists manually curated the database and this information was used to improve the automated detection and annotation of integrons and their encoded gene cassettes. ACID (annotation of cassette and integron data) can be searched using a range of queries and the data can be downloaded in a number of formats. Users can readily annotate their own data and integrate it into ACID using the tools provided.
  
  
  CONCLUSIONS
  ACID is a community resource providing easy access to annotations of integrons and making tools available to detect them in novel sequence data. ACID also hosts a forum to prompt integron-related discussion, which can hopefully lead to a more universal definition of this genetic element.
authors.affiliation: Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, 02139, USA. Michael.joss@gmail.com
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Joss
authors.forename: Jeremy E
authors.initials: JE
authors.lastname: Koenig
authors.forename: Maurizio
authors.initials: M
authors.lastname: Labbate
authors.forename: Martin F
authors.initials: MF
authors.lastname: Polz
authors.forename: Michael R
authors.initials: MR
authors.lastname: Gillings
authors.forename: Harold W
authors.initials: HW
authors.lastname: Stokes
authors.forename: W Ford
authors.initials: WF
authors.lastname: Doolittle
authors.forename: Yan
authors.initials: Y
authors.lastname: Boucher
mesh_terms: D000465:Algorithms; D030541:Databases, Genetic; D019143:Evolution, Molecular; D005798:Genes, Bacterial; D016680:Genome, Bacterial; D032023:Integrons