RAST protocols

RAST specifications

Information


Unique identifier OMICS_04222
Name RAST
Alternative names Rapid Annotation using Subsystem Technology, RAST Server
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Registration required Yes
Maintained Yes

Maintainer


  • person_outline Veronika Vonstein <>

Publications for Rapid Annotation using Subsystem Technology

RAST IN pipelines

 (198)
2018
PMCID: 5754496
PMID: 29301887
DOI: 10.1128/genomeA.01416-17

[…] draft genome completeness and contamination was assessed using checkm (13). the final draft genome was annotated using the ncbi prokaryotic genome annotation pipeline (pgap) (14) and reviewed using rast v2.0 (15)., this resulted in a 3.47-mbp draft genome estimated to be 93.9% complete with 1.79% potential contamination, comprising 5 scaffolds with a gc content of 36%, 3,354 coding sequences, […]

2018
PMCID: 5790007
PMID: 29382867
DOI: 10.1038/s41598-018-20135-4

[…] concisus whole genomes using a previously described method36. briefly, the 104 genomes from this study and an additional 9 c. concisus reference genomes were automatically annotated using the seed/rast system37,38 and a pangenome reference list of unique genes was assembled using blast with the following parameters: a sequence was considered to be an allelic variant of an existing gene […]

2018
PMCID: 5810265
PMID: 29472894
DOI: 10.3389/fmicb.2017.02679

[…] sequences of pufl and pufm genes were obtained in the present study from an ongoing genome project. genome sequences were annotated using the rapid annotations using subsystems technology (rast, aziz et al., 2008; overbeek et al., 2014). sequences of pufl and pufm were retrieved from the annotated genomes and deposited in the embl database under the accession numbers mf563614–mf563648, […]

2018
PMCID: 5834339
PMID: 29496843
DOI: 10.1128/genomeA.01487-17

[…] software (4). functional annotation was achieved using the blastp algorithm (5) against the clusters of orthologous groups (cogs) database and the rapid annotations using subsystems technology (rast) web server (6). ribosomal rnas (5s, 16s, and 23s rrnas) were predicted using rnammer software (7)., the genome was 1,672,788-bp long, assembled in five scaffolds (seven contigs) with a g+c […]

2018
PMCID: 5851621
PMID: 29538430
DOI: 10.1371/journal.pone.0194088

[…] not directly observed for the living, isolated sample but based on a generally accepted property for the species or anecdotal evidence). these evidence codes are from the gene ontology project., rast analysis predicted 5253 genes in total: 5179 protein encoding genes (pegs) and 74 rnas, of which 65 are trnas. 54.0% of pegs (2757) were arranged into 527 subsystems, and a total of 1125 […]

RAST institution(s)
Fellowship for Interpretation of Genomes, Burr Ridge, IL, USA; Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, USA; Computation Institute, University of Chicago, Chicago, IL, USA; Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Department of Computer Science, San Diego State University, San Diego, CA, USA; Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA, USA; Computing, Environment and Life Sciences, Argonne National Laboratory, Argonne, IL, USA; Department of Computer Science, University of Chicago, Chicago, IL, USA
RAST funding source(s)
Supported by United States National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Service [HHSN272200900040C], the National Science Foundation Grant [DBI-0850546], the Office of Science, Office of Biological and Environmental Research, of the United States Department of Energy [DE-AC02-06CH11357] and United States National Science Foundation Grant [DBI0850356] from the NSF Division of Biological Infrastructure (the PhAnToMe project).

RAST reviews

 (3)
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Korin Albert

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Web
I really like RAST...it's extremely easy to upload freshly-assembled genomes and get the quick and dirty info on them. Anyone could use this, including people with no genomics experience. It also serves as a great way to keep my genomics data on hand at all times from any computer. My only big issue is that their public genome database is too limited for my purposes (bifidobacteria) so their "identify related organisms" tool is useless to me. I have to upload most of the reference genomes I need myself.

Amr Galal

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Web
the tool is very useful for microbial and archeal genomes, easy, and good to save results