RAST protocols

View RAST computational protocol

RAST statistics

To access cutting-edge analytics on consensus tools, life science contexts and associated fields, you will need to subscribe to our premium service.

Subscribe
info

Citations per year

Citations chart
info

Popular tool citations

chevron_left Annotation workflows tRNA gene prediction SnoRNA gene prediction ORF detection chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

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

 (522)
2018
PMCID: 5754496
PMID: 29301887
DOI: 10.1128/genomeA.01416-17

[…] draft genome completeness and contamination was assessed using checkm (). the final draft genome was annotated using the ncbi prokaryotic genome annotation pipeline (pgap) () and reviewed using rast v2.0 ()., 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, 34 […]

2018
PMCID: 5762899
PMID: 29321512
DOI: 10.1038/s41598-017-18630-1

[…] and gca_000686085.1 (marinobacter hl-58). the genomes were annotated integrating information from the following pipelines: 1) the doe-jgi microbial genome annotation pipeline, blastkoala, and the rast server, as previously described. annotations are available on github (see below) and through img (http://img.jgi.doe.gov). the total number of protein encoding genes identified for halomonas […]

2018
PMCID: 5764924
PMID: 29326200
DOI: 10.1128/genomeA.01143-17

[…] annotation were conducted using glimmer version 3.02 (), prodigal version 1.20 (), genemarks version 4.08 (), and protein blast () and confirmed by the rapid annotations using subsystems technology (rast) version 2.0 server (). trnas were predicted using trnascan-se version 2.0 (), and the nucleotide homology of pvco-5 was determined using emboss stretcher ()., the genome of pvco-5 comprised […]

2018
PMCID: 5764942
PMID: 29326218
DOI: 10.1128/genomeA.01435-17

[…] on a miseq sequencer (illumina, inc., san diego, ca, usa) using the paired-end strategy. raw reads were assembled with a5-miseq software (). genome and subsystem-based annotations were performed by rapid annotation using subsystem technology (rast) (, ). trna gene detection was performed using the trnascan-se 2.0 tool (), whereas rrna genes were predicted using rnammer (). plasmid presence […]

2018
PMCID: 5764946
PMID: 29326222
DOI: 10.1128/genomeA.01453-17

[…] contig was 455,093 bp, and the shortest contig was 2,842 bp. the assembly produced an estimated genome of approximately 2.36 mb, with 40.7% g+c content. an initial gene inspection was made with the rapid annotation using subsystem technology (rast) pipeline (). finally, automatic gene prediction and annotation were performed using the ncbi prokaryotic genome annotation pipeline […]


To access a full list of citations, you will need to upgrade to our premium service.

RAST in publications

 (2046)
PMCID: 5955891
PMID: 29769695
DOI: 10.1038/s41598-018-26073-5

[…] assembled de novo using spades algorithm (spades version 3.7.1) for illumina-derived reads and then manually curated to close the gaps. putative open reading frames (orfs) were identified by rast version 2.0 and manually curated when necessary. blastp analyses of the putative orfs against the ncbi non-redundant proteins (nr) database, pfam, and interpro scan were used to assess […]

PMCID: 5953950
PMID: 29765033
DOI: 10.1038/s41426-018-0089-y

[…] ordering and manual curation was conducted using geneious mapper with high sensitivity and up to five times iteration in geneious 10 workbench, following automated annotation of draft genomes in rast. genomes are deposited in genbank under cp025423-cp025424 for horse_pl chromosome and plasmid, and pjpx00000000 for 10652_placenta; pjpy00000000 for 9945_foetus, pjpz00000000 for 8882_foetus […]

PMCID: 5946035
PMID: 29748397
DOI: 10.1128/genomeA.00229-18

[…] (7 genes for 5s, 6 for 16s, and 6 for 23s), 60 trnas, and 4 noncoding rnas. a total of 108 pseudogenes were predicted. functional annotation using the rapid annotations using subsystems technology (rast) server () revealed that 75 of the genes were associated with virulence, disease, and defense, 140 genes with rna metabolism, 196 genes with carbohydrate metabolism, and 259 genes […]

PMCID: 5944007
PMID: 29760866
DOI: 10.1186/s40793-018-0316-0

[…] of each contig (unitig_0: 4,903,991; unitig_1: 123,705; unitig_2: 118,720; unitig_3: 30,364); the final sizes are reported in table .table 3, the complete genome sequence was annotated with the rast server [] which predicted 5028 coding sequences and 110 rnas., a summary of the genome of e. coli 1094 is included in table . the genome statistics are provided in table . three putative […]

PMCID: 5943477
PMID: 29774012
DOI: 10.3389/fmicb.2018.00839

[…] (). the draft genome sequence of p. hydrolytica s66t is available from genbank, acc. no. lsne00000000 (). the results presented here are based on protein predictions and locus tags generated by rast (), and are accessible on the rast guest account under genome id 89404.4 (using login and password ‘guest’). for convenience the rast generated locus tag prefix (fig|89404.4.peg.) was renamed […]


To access a full list of publications, you will need to upgrade to our premium service.

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)
star_border star_border star_border star_border star_border
star star star star star

Korin Albert

star_border star_border star_border star_border star_border
star star star star star
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

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