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Info: NOTICE: RAST is Back Online (sort of)

The RAST system is back online (sort of). Several of the nodes that ran services that RAST depends on failed to reboot after the scheduled downtime, and had to be repaired or replaced. In particular, the BLAST compute-cluster will be down for some time, causing all RASTtk jobs to stall at the BLAST step, and crippling RAST's throughput for "Classic RAST", . :-(

After some deliberation, we have relectantly elected to disable the BLAST stage of RAST rather than allow jobs to accumulate, so that at least jobs will be able to run to completion minus BLAST similarities.

The main impacts that disabling similarities will have are that:
1.) Genes in "Classic RAST" jobs with no Kmer hits and whose translations are not already in our nonredundant database will be annotated "Hypothetical protein".
2.) Genes whose translations are not already in our nonredundant database will not be able to retrieve homologous regions in other genomes within the "Compare Regions" display of the SEED-Viewer.

If a gene did have Kmer hits and could be placed into a PATtyFam, we can partially compensate for (2.) above by constructing "Compare Regions" based on PATtyFam membership rather than BLAST similarity, so we will switch "Compare Regions" to default to aligning regions based on PATtyFam membership.

If you feel you do need BLAST sims against the NR and/or BLAST-based SEED-viewer comparions, you should select "Classic RAST" rather than default to RASTtk — but be advised that, because BLAST throughput is crippled, "Classic RAST" jobs are going to run slower than usual. :-(

We are continuing to work on the system, and we hope to bring RAST back to full capacity as soon as the compute cluster can be restored. (We are also working on a stopgap measure that will compute BLAST similarities against just the nearest-neighbor genomes, but it will probably be at least a week before that feature can go "live".)

We apologize that the scheduled maintenance outage took longer than originally anticipated and that the system did not come back up cleanly afterwards. We thank you for your patience during RAST's recovery period.

To monitor RAST's load and view other news and statistics for RAST and the SEED, please visit "The Daily SEED."

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RAST Job Load, last 24 hours

What is RAST?

RAST (Rapid Annotation using Subsystem Technology) is a fully-automated service for annotating complete or nearly complete bacterial and archaeal genomes. It provides high quality genome annotations for these genomes across the whole phylogenetic tree.

We have a number of presentations and tutorials available:

As the number of more or less complete bacterial and archaeal genome sequences is constantly rising, the need for high quality automated initial annotations is rising with it. In response to numerous requests for a SEED-quality automated annotation service, we provide RAST as a free service to the community. It leverages the data and procedures established within the SEED framework to provide automated high quality gene calling and functional annotation. RAST supports both the automated annotation of high quality genome sequences AND the analysis of draft genomes. The service normally makes the annotated genome available within 12-24 hours of submission.

Please note that while the SEED environment and SEED data structures (most prominently FIGfams) are used to compute the automatic annotations, the data is NOT added into the SEED automatically. Users can however request inclusion of a their genome in the SEED. Once annotation is completed, genomes can be downloaded in a variety of formats or viewed online. The genome annotation provided does include a mapping of genes to subsystems and a metabolic reconstruction.

To be able to contact you once the computation is finished and in case user intervention is required, we request that users register with email address.

If you use the results of this annotation in your work, please cite:

This project has been funded in whole or in part with Federal funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, under Contract No. HHSN272200900040C and the National Science Foundation under Grant No. 0850546.