MIT Libraries logoDSpace@MIT

MIT
View Item 
  • DSpace@MIT Home
  • MIT Open Access Articles
  • MIT Open Access Articles
  • View Item
  • DSpace@MIT Home
  • MIT Open Access Articles
  • MIT Open Access Articles
  • View Item
JavaScript is disabled for your browser. Some features of this site may not work without it.

ACID: annotation of cassette and integron data

Author(s)
Boucher, Yan; Labbate, Maurizio; Polz, Martin F.; Doolittle, W. Ford; Stokes, Harold W.; Gillings, Michael R.; Polz, Martin F.; Koenig, Jeremy E.; Joss, Michael J.; ... Show more Show less
Thumbnail
DownloadJoss-2009-ACID_ annotation of.pdf (386.5Kb)
PUBLISHER_CC

Publisher with Creative Commons License

Creative Commons Attribution

Terms of use
Creative Commons Attribution http://creativecommons.org/licenses/by/2.0/
Metadata
Show full item record
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.
Date issued
2009-04
URI
http://hdl.handle.net/1721.1/52515
Department
Massachusetts Institute of Technology. Department of Civil and Environmental Engineering
Journal
BMC Bioinformatics
Publisher
BioMed Central
Citation
Joss, Michael et al. “ACID: annotation of cassette and integron data.” BMC Bioinformatics 10.1 (2009): 118.
Version: Final published version
ISSN
1471-2105

Collections
  • MIT Open Access Articles

Browse

All of DSpaceCommunities & CollectionsBy Issue DateAuthorsTitlesSubjectsThis CollectionBy Issue DateAuthorsTitlesSubjects

My Account

Login

Statistics

OA StatisticsStatistics by CountryStatistics by Department
MIT Libraries
PrivacyPermissionsAccessibilityContact us
MIT
Content created by the MIT Libraries, CC BY-NC unless otherwise noted. Notify us about copyright concerns.