The RAST Server: Rapid annotations using subsystems technology

Ramy K. Aziz, Daniela Bartels, Aaron Best, Matthew DeJongh, Terrence Disz, Robert A. Edwards, Kevin Formsma, Svetlana Gerdes, Elizabeth M. Glass, Michael Kubal, Folker Meyer, Gary J. Olsen, Robert Olson, Andrei L. Osterman, Ross A. Overbeek, Leslie K. McNeil, Daniel Paarmann, Tobias Paczian, Bruce Parrello, Gordon D. PuschClaudia Reich, Rick Stevens, Olga Vassieva, Veronika Vonstein, Andreas Wilke, Olga Zagnitko

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Article number75
JournalBMC genomics
Volume9
DOIs
StatePublished - Feb 8 2008

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Genome
Technology
Archaeal Genome
Bacterial Genomes
Transfer RNA
Metabolic Networks and Pathways
rRNA Genes
Genes
Proteins

ASJC Scopus subject areas

  • Biotechnology
  • Genetics

Cite this

Aziz, R. K., Bartels, D., Best, A., DeJongh, M., Disz, T., Edwards, R. A., ... Zagnitko, O. (2008). The RAST Server: Rapid annotations using subsystems technology. BMC genomics, 9, [75]. https://doi.org/10.1186/1471-2164-9-75

The RAST Server : Rapid annotations using subsystems technology. / Aziz, Ramy K.; Bartels, Daniela; Best, Aaron; 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.

In: BMC genomics, Vol. 9, 75, 08.02.2008.

Research output: Contribution to journalArticle

Aziz, RK, Bartels, D, Best, A, DeJongh, M, Disz, T, Edwards, RA, Formsma, K, Gerdes, S, Glass, EM, Kubal, M, Meyer, F, Olsen, GJ, Olson, R, Osterman, AL, Overbeek, RA, McNeil, LK, Paarmann, D, Paczian, T, Parrello, B, Pusch, GD, Reich, C, Stevens, R, Vassieva, O, Vonstein, V, Wilke, A & Zagnitko, O 2008, 'The RAST Server: Rapid annotations using subsystems technology', BMC genomics, vol. 9, 75. https://doi.org/10.1186/1471-2164-9-75
Aziz RK, Bartels D, Best A, DeJongh M, Disz T, Edwards RA et al. The RAST Server: Rapid annotations using subsystems technology. BMC genomics. 2008 Feb 8;9. 75. https://doi.org/10.1186/1471-2164-9-75
Aziz, Ramy K. ; Bartels, Daniela ; Best, Aaron ; 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. / The RAST Server : Rapid annotations using subsystems technology. In: BMC genomics. 2008 ; Vol. 9.
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