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Title: The RAST server : rapid annotations using subsystems technology.

Abstract

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. 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.

Authors:
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Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States)
Sponsoring Org.:
USDOE Office of Science (SC); National Institutes of Health (NIH)
OSTI Identifier:
927765
Report Number(s):
ANL/MCS/JA-61372
TRN: US200816%%1258
DOE Contract Number:  
DE-AC02-06CH11357
Resource Type:
Journal Article
Journal Name:
BMC Genomics
Additional Journal Information:
Journal Volume: 9; Journal Issue: Feb. 8. 2008
Country of Publication:
United States
Language:
ENGLISH
Subject:
59 BASIC BIOLOGICAL SCIENCES; ACCURACY; GENES; ANL

Citation Formats

Aziz, R K, Bartels, D, Best, A A, DeJongh, M, Disz, T, Edwards, R A, Formsma, K, Gerdes, S, Glass, E M, Kubal, M, Meyer, F, Olsen, G J, Olson, R, Osterman, A L, Overbeek, R A, McNeil, L K, Paarmann, D, Paczian, T, Parrello, B, Pusch, G D, Reich, C, Stevens, R, Vassieva, O, Vonstein, V, Wilke, A, Zagnitko, O, Mathematics and Computer Science, Fellowship for Interpretation of Genomes, Univ. of Chicago, Univ. of Illinois, The Burnham Inst., Hope, Coll, Univ. of Tenn., and Cairo Univ. The RAST server : rapid annotations using subsystems technology.. United States: N. p., 2008. Web. doi:10.1186/1471-2164-9-75.
Aziz, R K, Bartels, D, Best, A A, DeJongh, M, Disz, T, Edwards, R A, Formsma, K, Gerdes, S, Glass, E M, Kubal, M, Meyer, F, Olsen, G J, Olson, R, Osterman, A L, Overbeek, R A, McNeil, L K, Paarmann, D, Paczian, T, Parrello, B, Pusch, G D, Reich, C, Stevens, R, Vassieva, O, Vonstein, V, Wilke, A, Zagnitko, O, Mathematics and Computer Science, Fellowship for Interpretation of Genomes, Univ. of Chicago, Univ. of Illinois, The Burnham Inst., Hope, Coll, Univ. of Tenn., & Cairo Univ. The RAST server : rapid annotations using subsystems technology.. United States. https://doi.org/10.1186/1471-2164-9-75
Aziz, R K, Bartels, D, Best, A A, DeJongh, M, Disz, T, Edwards, R A, Formsma, K, Gerdes, S, Glass, E M, Kubal, M, Meyer, F, Olsen, G J, Olson, R, Osterman, A L, Overbeek, R A, McNeil, L K, Paarmann, D, Paczian, T, Parrello, B, Pusch, G D, Reich, C, Stevens, R, Vassieva, O, Vonstein, V, Wilke, A, Zagnitko, O, Mathematics and Computer Science, Fellowship for Interpretation of Genomes, Univ. of Chicago, Univ. of Illinois, The Burnham Inst., Hope, Coll, Univ. of Tenn., and Cairo Univ. 2008. "The RAST server : rapid annotations using subsystems technology.". United States. https://doi.org/10.1186/1471-2164-9-75.
@article{osti_927765,
title = {The RAST server : rapid annotations using subsystems technology.},
author = {Aziz, R K and Bartels, D and Best, A A and DeJongh, M and Disz, T and Edwards, R A and Formsma, K and Gerdes, S and Glass, E M and Kubal, M and Meyer, F and Olsen, G J and Olson, R and Osterman, A L and Overbeek, R A and McNeil, L K and Paarmann, D and Paczian, T and Parrello, B and Pusch, G D and Reich, C and Stevens, R and Vassieva, O and Vonstein, V and Wilke, A and Zagnitko, O and Mathematics and Computer Science and Fellowship for Interpretation of Genomes and Univ. of Chicago and Univ. of Illinois and The Burnham Inst. and Hope, Coll and Univ. of Tenn. and Cairo Univ.},
abstractNote = {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. 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.},
doi = {10.1186/1471-2164-9-75},
url = {https://www.osti.gov/biblio/927765}, journal = {BMC Genomics},
number = Feb. 8. 2008,
volume = 9,
place = {United States},
year = {Fri Feb 08 00:00:00 EST 2008},
month = {Fri Feb 08 00:00:00 EST 2008}
}