The RAST Server: Rapid Annotations using Subsystems Technology View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2008-02-08

AUTHORS

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

ABSTRACT

BackgroundThe number of prokaryotic genome sequences becoming available is growing steadily and is growing faster than our ability to accurately annotate them.DescriptionWe 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.ConclusionBy 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. More... »

PAGES

75

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/1471-2164-9-75

DOI

http://dx.doi.org/10.1186/1471-2164-9-75

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1013431920

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/18261238


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    "description": "BackgroundThe number of prokaryotic genome sequences becoming available is growing steadily and is growing faster than our ability to accurately annotate them.DescriptionWe 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\u201324 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.ConclusionBy 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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N-Triples is a line-based linked data format ideal for batch operations.

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Turtle is a human-readable linked data format.

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RDF/XML is a standard XML format for linked data.

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1186/1471-2164-9-75'


 

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359 grid-institutes:grid.479509.6 schema:alternateName The Burnham Institute, 92037, San Diego, CA, USA
360 schema:name Fellowship for Interpretation of Genomes, 60527, Burr Ridge, IL, USA
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363 grid-institutes:grid.505692.d schema:alternateName National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, 61801, Urbana, IL, USA
364 schema:name National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, 61801, Urbana, IL, USA
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366 grid-institutes:grid.7776.1 schema:alternateName Department of Microbiology and Immunology, Cairo University, Cairo, Egypt
367 schema:name Department of Microbiology and Immunology, Cairo University, Cairo, Egypt
368 University of Tennessee, Health Science Center, 38136, Memphis, TN, USA
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