The RAST Server: Rapid Annotations using Subsystems Technology
<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 ser...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
BMC
2008-02-01
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| Series: | BMC Genomics |
| Online Access: | http://www.biomedcentral.com/1471-2164/9/75 |
| _version_ | 1811335061862088704 |
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| author | 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 |
| author_facet | 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 |
| author_sort | Overbeek Ross A |
| collection | DOAJ |
| description | <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> |
| first_indexed | 2024-04-13T17:18:26Z |
| format | Article |
| id | doaj.art-5cde187e56664b6d9716978b22e1144b |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-04-13T17:18:26Z |
| publishDate | 2008-02-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-5cde187e56664b6d9716978b22e1144b2022-12-22T02:38:03ZengBMCBMC Genomics1471-21642008-02-01917510.1186/1471-2164-9-75The RAST Server: Rapid Annotations using Subsystems TechnologyOverbeek Ross AOsterman Andrei LOlson RobertOlsen Gary JMeyer FolkerKubal MichaelGlass Elizabeth MGerdes SvetlanaFormsma KevinEdwards Robert ADisz TerrenceDeJongh MatthewBest Aaron ABartels DanielaAziz Ramy KMcNeil Leslie KPaarmann DanielPaczian TobiasParrello BrucePusch Gordon DReich ClaudiaStevens RickVassieva OlgaVonstein VeronikaWilke AndreasZagnitko Olga<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>http://www.biomedcentral.com/1471-2164/9/75 |
| spellingShingle | 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 The RAST Server: Rapid Annotations using Subsystems Technology BMC Genomics |
| title | The RAST Server: Rapid Annotations using Subsystems Technology |
| title_full | The RAST Server: Rapid Annotations using Subsystems Technology |
| title_fullStr | The RAST Server: Rapid Annotations using Subsystems Technology |
| title_full_unstemmed | The RAST Server: Rapid Annotations using Subsystems Technology |
| title_short | The RAST Server: Rapid Annotations using Subsystems Technology |
| title_sort | rast server rapid annotations using subsystems technology |
| url | http://www.biomedcentral.com/1471-2164/9/75 |
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