RAST pipeline

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

 (44)
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: 5872301
PMID: 29600285
DOI: 10.1128/mSystems.00195-17

[…] for the plasmid) using bowtie 2 version 2.2.6 (34). sequence data were de novo assembled using spades version 3.8.0 (35), and functional annotations were obtained for contigs of interest using rast (36). regions of similarity between host and clone dna were identified using mauve (37). data analyses were performed in r, including packages rsamtools, gviz, ape, and genoplotr., raw sequence […]

2017
PMCID: 5331506
PMID: 28183766
DOI: 10.1128/genomeA.01598-16

[…] 7.5). the bb01 genome (1,271× coverage) had a g+c content of 51.8%, with 2,517,579 bp distributed among 84 contigs ranging in size from 1,006 bp to 197,455 bp. annotation was performed by the rast server (http://rast.nmpdr.org/) (5). the bb01 genome was predicted to have a total of 2,943 open reading frames (orfs) and 48 rna genes., to evaluate the subspecies status of bb01 strain, […]

2017
PMCID: 5561048
PMID: 28819148
DOI: 10.1038/s41598-017-08735-y

[…] the blast tool to investigate the presence of several different r391 (ay090559) and sxt (ay055428) core scaffold genes (int, jef, tralekbva, setcd). the r997 sequence was then annotated using the rast server (rapid annotation using subsystem technology) and the basic local alignment search tool (blast) programme at ncbi31, 32. any gaps among the sequence were filled in by pcr-linkage […]

2017
PMCID: 5626979
PMID: 29033917
DOI: 10.3389/fmicb.2017.01870

[…] whole genome assembly was performed with the gs de novo assembler using default parameters (microsynth). the fully assembled genome was annotated using rapid annotations using subsystems technology (rast) (aziz et al., 2008; overbeek et al., 2014; brettin et al., 2015) and the default setting options. additionally, genome annotation was verified and curated by blast analysis (altschul et al., […]

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