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

By R. Overbeek, R. Olson, G. Pusch, G. Olsen, James J. Davis, T. Disz, Robert A. Edwards, S. Gerdes, B. Parrello, Maulik Shukla and 4 more. Nucleic Acids Res., 2013

4,312 citations recorded by the source corpus.

In 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.

Subfields: Biomedical Engineering, Molecular Biology

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Citations in the corpus

Expanded microbial genome coverage and improved protein family annotation in the COG database (2014, methodology): “Subsequently, COG annotations were included into the SEED database (4) and the possibility to compare newly sequenced genomes against COGs had been provided by the Integrated Microbial Genomes (IMG) system at the DOE’s Joint Genome Institute (5).”
RefSeq: expanding the Prokaryotic Genome Annotation Pipeline reach with protein family model curation (2020, methodology): “We are exploring using PFMs from more sources, including UniProt’s UniRules (24), and fine-tuning together the coverage of PFMs that are linked to a single biological process, in the manner of Genome Properties (12,25) and RAST (26).”
A genomic catalog of Earth’s microbiomes (2020, methodology): “GEMs and reference genomes were annotated with RAST [6] in KBase, as the ModelSEED pipeline uses RAST functional roles to map genes to biochemical reactions [7, 8] .”
MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data (2016, methodology): “MEGAN CE offers a SEED analyzer based on the concepts of subsystems and functional roles [14] and an eggNOG viewer based on the eggNOG extension of COGs [15].”
The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities (2019, background): “Subsystems are collections of functionally re-lated proteins and are a vital conceptual device for identifying and projecting protein functions across species (7,52).”
proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes (2016, background): “The extensive use of genome sequencing in microbiology has led to an exponential increase in the number of sequenced bacteria and archaea (4) (Figure 1).”
Probiotics, gut microbiota, and their influence on host health and disease (2017, methodology): “[124] Overbeek, R., Olson, R., Pusch, G. D., Olsen, G. J. et al., The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST).”
Systematic genome assessment of B-vitamin biosynthesis suggests co-operation among gut microbes (2015, methodology): “The PubSEED platform (http://pubseed.theseed.org/) (Overbeek et al., 2005, 2013; Disz et al., 2010) contains fully annotated subsystems for eight B-vitamins: biotin, cobalamin, folate, niacin, pantothenate, pyridoxine, riboflavin, and thiamin (Table 1).”
Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper (2016, methodology): “Most tools in use for functional annotation of newly sequenced genomes apply BLAST (Blast2GO, Go¨tz et al. 2008; RAST, Overbeek et al. 2014) or sequence profile-based searches (Finn et al. 2014; Jones et al. 2014) to transfer functional terms from homologous sequences.”
VICTOR: genome-based phylogeny and classification of prokaryotic viruses (2017, methodology): “A larger data set of 4419 phages was collected from GenBank and the PhAnToMe FTP server (as of July 2016) (Overbeek et al. 2014), without restriction to taxa recognized by the ICTV (Supplementary File S1).”
Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center (2016, methodology): “First, they are generated from the PubSEED database, which contains ∼ 12 000 genomes (45,46).”