The RAST Server: Rapid Annotations using Subsystems Technology

Springer Science and Business Media LLC - Tập 9 - Trang 1-15 - 2008
Ramy K Aziz1,2, Daniela Bartels3, Aaron A Best4, Matthew DeJongh4, Terrence Disz5,3, Robert A Edwards6,5, Kevin Formsma4, Svetlana Gerdes6, Elizabeth M Glass5, Michael Kubal3, Folker Meyer5,3, Gary J Olsen7,5, Robert Olson5,3, Andrei L Osterman6,8, Ross A Overbeek6, Leslie K McNeil9, Daniel Paarmann3, Tobias Paczian3, Bruce Parrello6, Gordon D Pusch6,3, Claudia Reich9, Rick Stevens5,3, Olga Vassieva6, Veronika Vonstein6, Andreas Wilke3, Olga Zagnitko6
1University of Tennessee Health Science Center, Memphis, USA
2Department of Microbiology and Immunology, Cairo University, Cairo, Egypt
3Computation Institute, University of Chicago, Chicago, USA
4Hope College, Holland, USA
5Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, USA
6Fellowship for Interpretation of Genomes, Burr Ridge, USA
7Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, USA
8The Burnham Institute, San Diego, USA
9National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, USA

Tóm tắt

The number of prokaryotic genome sequences becoming available is growing steadily and is growing faster than our ability to accurately annotate them. We describe a fully automated service for annotating bacterial and archaeal genomes. The service identifies protein-encoding, rRNA and tRNA genes, assigns functions to the genes, predicts which subsystems are represented in the genome, uses this information to reconstruct the metabolic network and makes the output easily downloadable for the user. In addition, the annotated genome can be browsed in an environment that supports comparative analysis with the annotated genomes maintained in the SEED environment. The service normally makes the annotated genome available within 12–24 hours of submission, but ultimately the quality of such a service will be judged in terms of accuracy, consistency, and completeness of the produced annotations. We summarize our attempts to address these issues and discuss plans for incrementally enhancing the service. By providing accurate, rapid annotation freely to the community we have created an important community resource. The service has now been utilized by over 120 external users annotating over 350 distinct genomes.

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