The RAST Server: Rapid Annotations using Subsystems Technology

BMC Genomics. 2008;9(1):75 DOI 10.1186/1471-2164-9-75

 

Journal Homepage

Journal Title: BMC Genomics

ISSN: 1471-2164 (Online)

Publisher: BMC

LCC Subject Category: Technology: Chemical technology: Biotechnology | Science: Biology (General): Genetics

Country of publisher: United Kingdom

Language of fulltext: English

Full-text formats available: PDF, HTML

 

AUTHORS

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

EDITORIAL INFORMATION

Blind peer review

Editorial Board

Instructions for authors

Time From Submission to Publication: 17 weeks

 

Abstract | Full Text

<p>Abstract</p> <p>Background</p> <p>The number of prokaryotic genome sequences becoming available is growing steadily and is growing faster than our ability to accurately annotate them.</p> <p>Description</p> <p>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.</p> <p>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.</p> <p>Conclusion</p> <p>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.</p>