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The RAST Server: Rapid Annotations using Subsystems Technology

Open access
Aziz, Ramy K, Bartels, Daniela, Best, Aaron A, DeJongh, Matthew, Disz, Terrence, Edwards, Robert A, Formsma, Kevin, Gerdes, Svetlana, Glass, Elizabeth M, Kubal, Michael, Meyer, Folker, Olsen, Gary J, Olson, Robert, Osterman, Andrei L, Overbeek, Ross A, McNeil, Leslie K, Paarmann, Daniel, Paczian, Tobias, Parrello, Bruce, Pusch, Gordon D, Reich, Claudia, Stevens, Rick, Vassieva, Olga, Vonstein, Veronika, Wilke, Andreas, Zagnitko, Olga·2008·BMC Genomics
DOI 10.1186/1471-2164-9-75
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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.

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Research works printed but not linked: 21

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Metadata

Authors
Aziz, R. K., Bartels, D., Best, A. A., DeJongh, M., Disz, T., Edwards, R. A., Formsma, K., Gerdes, S., Glass, E. M., Kubal, M., Meyer, F., Olsen, G. J., Olson, R., Osterman, A. L., Overbeek, R. A., McNeil, L. K., Paarmann, D., Paczian, T., Parrello, B., Pusch, G. D., Reich, C., Stevens, R., Vassieva, O., Vonstein, V., Wilke, A., & Zagnitko, O.
Venue
BMC Genomics
Publisher
Springer Science and Business Media LLC
Published
2008-02-08
Volume
9
Issue
1
Pages
75-75
ISSN
1471-2164 (ISSN-L)
DOI
10.1186/1471-2164-9-75
OpenAlex
W2004548026
Cited by
11,729
References
0
FWCI
40.95
Type
journal article
Language
en
Open access
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CoChat. (2026). Citation check: The RAST Server: Rapid Annotations using Subsystems Technology. https://app.cochat.ai/papers/10.1186/1471-2164-9-75
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Aziz, R. K., Bartels, D., Best, A. A., DeJongh, M., Disz, T., Edwards, R. A., Formsma, K., Gerdes, S., Glass, E. M., Kubal, M., Meyer, F., Olsen, G. J., Olson, R., Osterman, A. L., Overbeek, R. A., McNeil, L. K., Paarmann, D., Paczian, T., Parrello, B., . . . Zagnitko, O. (2008). The RAST Server: Rapid Annotations using Subsystems Technology. BMC Genomics. https://doi.org/10.1186/1471-2164-9-75

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