Abstract
BackgroundAlthough 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.DescriptionBy 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.ConclusionACID 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.
Highlights
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
For the initial construction of the database; we have developed basic definitions for the different elements of integrons: the integron-encoded integrase, recombination sites attI and attC, gene cassettes, gene cassette open reading frames (CassORFs) and more generally, ORFs
We have provided the user with the option of searching for ORFs in any given DNA sequence regardless of its nature
Summary
Very few integrons have been properly identified and annotated in public databases These genetic elements have been overlooked in comparison to other vectors that facilitate LGT between microorganisms. The manually curated and publicly available web-based database can perform automated detection and annotation of integrons and gene cassettes enabling future sequence data to be incorporated . Users can readily annotate and save their own data and have the option of forwarding it to curators for addition to the main database. This database will help create more accurate annotations of bacterial genomes and facilitate a more representative sample of integron frequency and diversity. MFP provided sequence data for the database and contributed to the coordination of the study
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