RAST statistics

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Citations per year

Number of citations per year for the bioinformatics software tool RAST
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Tool usage distribution map

This map represents all the scientific publications referring to RAST per scientific context
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Associated diseases

This word cloud represents RAST usage per disease context
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Popular tool citations

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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 citations

 (2244)
library_books

An epizootic of Chlamydia psittaci equine reproductive loss associated with suspected spillover from native Australian parrots

2018
PMCID: 5953950
PMID: 29765033
DOI: 10.1038/s41426-018-0089-y

[…] ntig 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 and […]

call_split

Genomic and functional characterisation of IncX3 plasmids encoding blaSHV 12 in Escherichia coli from human and animal origin

2018
Sci Rep
PMCID: 5955891
PMID: 29769695
DOI: 10.1038/s41598-018-26073-5
call_split See protocol

[…] equently 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 their puta […]

call_split

Complete Genome Sequence of Staphylococcus haemolyticus Type Strain SGAir0252

2018
Genome Announc
PMCID: 5946035
PMID: 29748397
DOI: 10.1128/genomeA.00229-18
call_split See protocol

[…] s (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 with metabolism […]

library_books

High Quality Draft Single Cell Genome Sequence Belonging to the Archaeal Candidate Division SA1, Isolated from Nereus Deep in the Red Sea

2018
Genome Announc
PMCID: 5946040
PMID: 29748404
DOI: 10.1128/genomeA.00383-18

[…] tamination), based on operational standards for SAGs (), and contains 1,646 protein-coding genes plus 40 RNA-coding genes annotated with PGAP () and the Rapid Annotations using Subsystems Technology (RAST) server (). The SAG contained a 16S rRNA gene sequence with 99% identity to environmental SA1 sequences from DHABs but only 93% identity to Methanonatronarchaeia representatives (). Also, all thr […]

call_split

Identification and pathogenomic analysis of an Escherichia coli strain producing a novel Shiga toxin 2 subtype

2018
Sci Rep
PMCID: 5928088
PMID: 29712985
DOI: 10.1038/s41598-018-25233-x
call_split See protocol

[…] The sequence of the Stx converting phage was extracted from the complete genome by using the PHASTER (http://phaster.ca/), the genome of Stx converting phage was reannotated using the RAST server (http://rast.nmpdr.org/), and then manually verified and corrected. Functional annotation of selected CDSs was performed based on the results of homology searches against the public nonred […]

library_books

Lignite coal burning seam in the remote Altai Mountains harbors a hydrogen driven thermophilic microbial community

2018
Sci Rep
PMCID: 5928048
PMID: 29712968
DOI: 10.1038/s41598-018-25146-9

[…] ry phylogenetic assignment of obtained composite genomes were assessed with CheckM. For each composite genome, gene search and annotation were performed for all contigs longer than 2000 bp, using the RAST server, followed by manual correction by searching the National Center for Biotechnology Information (NCBI) databases. The 16S ribosomal RNA genes were found in contigs by CheckM. The search for […]


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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