The RAST Server: rapid annotations using subsystems technology.
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.
Aziz
Ramy K
RK
Fellowship for Interpretation of Genomes, Burr Ridge, IL 60527, USA. ramy.aziz@gmail.com
Bartels
Daniela
D
Best
Aaron A
AA
DeJongh
Matthew
M
Disz
Terrence
T
Edwards
Robert A
RA
Formsma
Kevin
K
Gerdes
Svetlana
S
Glass
Elizabeth M
EM
Kubal
Michael
M
Meyer
Folker
F
Olsen
Gary J
GJ
Olson
Robert
R
Osterman
Andrei L
AL
Overbeek
Ross A
RA
McNeil
Leslie K
LK
Paarmann
Daniel
D
Paczian
Tobias
T
Parrello
Bruce
B
Pusch
Gordon D
GD
Reich
Claudia
C
Stevens
Rick
R
Vassieva
Olga
O
Vonstein
Veronika
V
Wilke
Andreas
A
Zagnitko
Olga
O
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
D011506:Proteins; D012343:RNA, Transfer