ACID

annotation of cassette and integron data

Michael J. Joss, Jeremy E. Koenig, Maurizio Labbate, Martin F. Polz, Michael R. Gillings, Harold W. Stokes, W. Ford Doolittle, Yan Boucher*

*Corresponding author for this work

Research output: Contribution to journalArticle

28 Citations (Scopus)
19 Downloads (Pure)

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. Description: 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. Conclusion: 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.

Original languageEnglish
Article number118
Pages (from-to)1-9
Number of pages9
JournalBMC Bioinformatics
Volume10
DOIs
Publication statusPublished - 21 Apr 2009

Bibliographical note

Copyright 2009 Joss et al; licensee BioMed Central Ltd. Version archived for private and non-commercial use with the permission of the author and according to publisher conditions. For further rights please contact the publisher.

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