Ramy K Aziz 8 , 9 , Daniela Bartels 3 , Aaron A Best 7 , Matthew DeJongh 7 , Terrence Disz 2 , 3 , Robert A Edwards 1 , 2 , Kevin Formsma 7 , Svetlana Gerdes 1 , Elizabeth M Glass 2 , Michael Kubal 3 , Folker Meyer 2 , 3 , Gary J Olsen 4 , 2 , Robert Olson 2 , 3 , Andrei L Osterman 1 , 5 , Ross A Overbeek , 1 , Leslie K McNeil 6 , Daniel Paarmann 3 , Tobias Paczian 3 , Bruce Parrello 1 , Gordon D Pusch 1 , 3 , Claudia Reich 6 , Rick Stevens 2 , 3 , Olga Vassieva 1 , Veronika Vonstein 1 , Andreas Wilke 3 , Olga Zagnitko 1
8 February 2008
The number of prokaryotic genome sequences becoming available is growing steadily and is growing faster than our ability to accurately annotate them.
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.