Maqola

The RAST Server: Rapid Annotations using Subsystems Technology

Ramy K. AzizFellowship for Interpretation of Genomes, Burr Ridge, IL 60527, USA. [email protected]Daniela BartelsComputation Institute, University of Chicago, Chicago, IL, 60637, USAAaron A. BestHope College, Holland, MI, 49423, USAMatthew DeJonghHope College, Holland, MI, 49423, USAT. DiszComputation Institute, University of Chicago, Chicago, IL, 60637, USARobert A. EdwardsFellowship for Interpretation of Genomes, Burr Ridge, IL, 60527, USAKevin FormsmaHope College, Holland, MI, 49423, USASvetlana GerdesElizabeth M. GlassMathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, 60439, USAMichael KubalComputation Institute, University of Chicago, Chicago, IL, 60637, USAFolker MeyerComputation Institute, University of Chicago, Chicago, IL, 60637, USAGary J. OlsenDepartment of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USARobert OlsonComputation Institute, University of Chicago, Chicago, IL, 60637, USAAndrei L. OstermanFellowship for Interpretation of Genomes, Burr Ridge, IL, 60527, USARoss OverbeekLeslie Klis McNeilNational Center for Supercomputing ApplicationsDaniel PaarmannComputation Institute, University of Chicago, Chicago, IL, 60637, USATobias PaczianComputation Institute, University of Chicago, Chicago, IL, 60637, USABruce ParrelloGordon D. PuschComputation Institute, University of Chicago, Chicago, IL, 60637, USAClaudia I. ReichNational Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USARick StevensComputation Institute, University of Chicago, Chicago, IL, 60637, USAOlga VassievaVeronika VonsteinAndreas WilkeComputation Institute, University of Chicago, Chicago, IL, 60637, USAOlga Zagnitko

2008en

ABI

Annotatsiya

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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DOI: 10.1186/1471-2164-9-75

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