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The RAST Server: rapid annotations using subsystems technology.

Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O - BMC Genomics (2008)

Bottom Line: 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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Fellowship for Interpretation of Genomes, Burr Ridge, IL 60527, USA. ramy.aziz@gmail.com

ABSTRACT

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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Job Detail page. The RAST annotation progress can be monitored by each user.
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Related In: Results  -  Collection

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Figure 4: Job Detail page. The RAST annotation progress can be monitored by each user.

Mentions: After login the user can monitor his/her submitted job/jobs on the Job Overview page (Figure 3). This page lists for each submitted job its number, submitter, the taxonomy ID and Genome name followed by a six-button bar, where each button represents a step in the RAST annotation service. Depending on the state of each step the button colour will change from grey (not started) to blue (queued for computation) to yellow (in progress) to green (successfully completed) or red (error) as shown in Figure 3. More detailed information about each step can be viewed after clicking the button bar itself. Figure 4 illustrates such a Job Detail page with the submission time stamp and the six steps. Here step one had been completed, step two was in progress and the other steps had not yet started.


The RAST Server: rapid annotations using subsystems technology.

Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O - BMC Genomics (2008)

Job Detail page. The RAST annotation progress can be monitored by each user.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2265698&req=5

Figure 4: Job Detail page. The RAST annotation progress can be monitored by each user.
Mentions: After login the user can monitor his/her submitted job/jobs on the Job Overview page (Figure 3). This page lists for each submitted job its number, submitter, the taxonomy ID and Genome name followed by a six-button bar, where each button represents a step in the RAST annotation service. Depending on the state of each step the button colour will change from grey (not started) to blue (queued for computation) to yellow (in progress) to green (successfully completed) or red (error) as shown in Figure 3. More detailed information about each step can be viewed after clicking the button bar itself. Figure 4 illustrates such a Job Detail page with the submission time stamp and the six steps. Here step one had been completed, step two was in progress and the other steps had not yet started.

Bottom Line: 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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Fellowship for Interpretation of Genomes, Burr Ridge, IL 60527, USA. ramy.aziz@gmail.com

ABSTRACT

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.

Show MeSH