The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)

Simple item page
dc.contributor.authorOverbeek, Rossen
dc.contributor.authorOlson, Roberten
dc.contributor.authorPusch, Gordon D.en
dc.contributor.authorOlsen, Gary J.en
dc.contributor.authorDavis, James J.en
dc.contributor.authorDisz, Terryen
dc.contributor.authorEdwards, Robert A.en
dc.contributor.authorGerdes, Svetlanaen
dc.contributor.authorParrello, Bruceen
dc.contributor.authorShukla, Mauliken
dc.contributor.authorVonstein, Veronikaen
dc.contributor.authorWattam, Alice R.en
dc.contributor.authorXia, Fangfangen
dc.contributor.authorStevens, Rick L.en
dc.date.accessioned2019-04-12T14:55:19Zen
dc.date.available2019-04-12T14:55:19Zen
dc.date.issued2014-01en
dc.description.abstractIn 2004, the SEED (http://pubseed.theseed.org/) was created to provide consistent and accurate genome annotations across thousands of genomes and as a platform for discovering and developing de novo annotations. The SEED is a constantly updated integration of genomic data with a genome database, web front end, API and server scripts. It is used by many scientists for predicting gene functions and discovering new pathways. In addition to being a powerful database for bioinformatics research, the SEED also houses subsystems (collections of functionally related protein families) and their derived FIGfams (protein families), which represent the core of the RAST annotation engine (http://rast.nmpdr.org/). When a new genome is submitted to RAST, genes are called and their annotations are made by comparison to the FIGfam collection. If the genome is made public, it is then housed within the SEED and its proteins populate the FIGfam collection. This annotation cycle has proven to be a robust and scalable solution to the problem of annotating the exponentially increasing number of genomes. To date, >12 000 users worldwide have annotated >60 000 distinct genomes using RAST. Here we describe the interconnectedness of the SEED database and RAST, the RAST annotation pipeline and updates to both resources.en
dc.description.notesUnited 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], as well as the Office of Science, Office of Biological and Environmental Research, of the United States Department of Energy [DE-AC02-06CH11357], as part of the DOE Systems Biology Knowledgebase. United States National Science Foundation Grant [DBI-0850356] (to R. A. E.) from the NSF Division of Biological Infrastructure (the PhAnToMe project). Funding for open access charge: National Institute of Allergy and Infectious Diseases.en
dc.description.sponsorshipUnited States National Institute of Allergy and Infectious Diseases; National Institutes of Health; Department of Health and Human Service [HHSN272200900040C]; National Science Foundation [DBI-0850546]; Office of Science, Office of Biological and Environmental Research, of the United States Department of Energy as part of the DOE Systems Biology Knowledgebase [DE-AC02-06CH11357]; United States National Science Foundation from the NSF Division of Biological Infrastructure (the PhAnToMe project) [DBI-0850356]; National Institute of Allergy and Infectious Diseasesen
dc.format.mimetypeapplication/pdfen
dc.identifier.doihttps://doi.org/10.1093/nar/gkt1226en
dc.identifier.eissn1362-4962en
dc.identifier.issn0305-1048en
dc.identifier.issueD1en
dc.identifier.pmid24293654en
dc.identifier.urihttp://hdl.handle.net/10919/88953en
dc.identifier.volume42en
dc.language.isoen_USen
dc.rightsCreative Commons Attribution 4.0 Internationalen
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.subjectdatabaseen
dc.subjectresourceen
dc.subjectdnaen
dc.subjectgenerationen
dc.subjectsequenceen
dc.subjectgenesen
dc.titleThe SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)en
dc.title.serialNucleic Acids Researchen
dc.typeArticle - Refereeden
dc.type.dcmitypeTexten

Files

Original bundle
Now showing 1 - 1 of 1
Thumbnail Image
Name:
gkt1226.pdf
Size:
3.17 MB
Format:
Adobe Portable Document Format
Description:
Download

Collections

Scholarly Works, Fralin Life Sciences Institute