title: The RAST Server: rapid annotations using subsystems technology.
abstract: BACKGROUND
  The number of prokaryotic genome sequences becoming available is growing steadily and is growing faster than our ability to accurately annotate them.
  
  
  METHODS
  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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Fellowship for Interpretation of Genomes, Burr Ridge, IL 60527, USA. ramy.aziz@gmail.com
authors.forename: Ramy K
authors.initials: RK
authors.lastname: Aziz
authors.forename: Daniela
authors.initials: D
authors.lastname: Bartels
authors.forename: Aaron A
authors.initials: AA
authors.lastname: Best
authors.forename: Matthew
authors.initials: M
authors.lastname: DeJongh
authors.forename: Terrence
authors.initials: T
authors.lastname: Disz
authors.forename: Robert A
authors.initials: RA
authors.lastname: Edwards
authors.forename: Kevin
authors.initials: K
authors.lastname: Formsma
authors.forename: Svetlana
authors.initials: S
authors.lastname: Gerdes
authors.forename: Elizabeth M
authors.initials: EM
authors.lastname: Glass
authors.forename: Michael
authors.initials: M
authors.lastname: Kubal
authors.forename: Folker
authors.initials: F
authors.lastname: Meyer
authors.forename: Gary J
authors.initials: GJ
authors.lastname: Olsen
authors.forename: Robert
authors.initials: R
authors.lastname: Olson
authors.forename: Andrei L
authors.initials: AL
authors.lastname: Osterman
authors.forename: Ross A
authors.initials: RA
authors.lastname: Overbeek
authors.forename: Leslie K
authors.initials: LK
authors.lastname: McNeil
authors.forename: Daniel
authors.initials: D
authors.lastname: Paarmann
authors.forename: Tobias
authors.initials: T
authors.lastname: Paczian
authors.forename: Bruce
authors.initials: B
authors.lastname: Parrello
authors.forename: Gordon D
authors.initials: GD
authors.lastname: Pusch
authors.forename: Claudia
authors.initials: C
authors.lastname: Reich
authors.forename: Rick
authors.initials: R
authors.lastname: Stevens
authors.forename: Olga
authors.initials: O
authors.lastname: Vassieva
authors.forename: Veronika
authors.initials: V
authors.lastname: Vonstein
authors.forename: Andreas
authors.initials: A
authors.lastname: Wilke
authors.forename: Olga
authors.initials: O
authors.lastname: Zagnitko
mesh_terms: D019295:Computational Biology / Q000379:methods*; D030561:Databases, Nucleic Acid; D020459:Genes, rRNA / Q000235:genetics; D020745:Genome, Archaeal; D016680:Genome, Bacterial; D016366:Open Reading Frames / Q000235:genetics; D010802:Phylogeny; D011506:Proteins / Q000235:genetics; D012343:RNA, Transfer / Q000235:genetics; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D013997:Time Factors; D014584:User-Computer Interface
chemical_list: D011506:Proteins; D012343:RNA, Transfer