Open Access Highly Accessed Database

The RAST Server: Rapid Annotations using Subsystems Technology

Ramy K Aziz89, Daniela Bartels3, Aaron A Best7, Matthew DeJongh7, Terrence Disz23, Robert A Edwards12, Kevin Formsma7, Svetlana Gerdes1, Elizabeth M Glass2, Michael Kubal3, Folker Meyer23, Gary J Olsen24, Robert Olson23, Andrei L Osterman15, Ross A Overbeek1*, Leslie K McNeil6, Daniel Paarmann3, Tobias Paczian3, Bruce Parrello1, Gordon D Pusch13, Claudia Reich6, Rick Stevens23, Olga Vassieva1, Veronika Vonstein1, Andreas Wilke3 and Olga Zagnitko1

Author affiliations

1 Fellowship for Interpretation of Genomes, Burr Ridge, IL 60527, USA

2 Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439, USA

3 Computation Institute, University of Chicago, Chicago, IL 60637, USA

4 Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA

5 The Burnham Institute, San Diego, CA 92037, USA

6 National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA

7 Hope College, Holland, MI 49423, USA

8 University of Tennessee, Health Science Center, Memphis, TN 38136, USA

9 Department of Microbiology and Immunology, Cairo University, Cairo, Egypt

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Citation and License

BMC Genomics 2008, 9:75  doi:10.1186/1471-2164-9-75

Published: 8 February 2008

Abstract

Background

The number of prokaryotic genome sequences becoming available is growing steadily and is growing faster than our ability to accurately annotate them.

Description

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.

Conclusion

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.