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

Abstract

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.

A Case of IMP-4-, OXA-421-, OXA-96-, and CARB-2-Producing Acinetobacterpittii Sequence Type 119 in Australia

“…We used the CLC genomic workbench version 7.5 (CLC Bio, Aarhus, Denmark) for de novo assembly with a 500-bp minimum threshold resulting in 127 contigs. The draft genome consisted of 4,372,178 nucleotides and was annotated by rapid annotations using subsystems technology (RAST) (12). RAST annotation showed that Acinetobacter calcoaceticus PHEA-2 (score, 503) and Acinetobacter sp.…”

Complete genome sequence of Planococcus donghaensis JH1T, a pectin-degrading bacterium

“…The reads were de novo assembled using the hierarchical genome assembly process (HGAP) algorithm version 2 (Chin et al, 2013) to generate the complete genome of P. donghaensis JH1 T , which consists of 2 polished contigs with an average genome coverage of 145.5 fold. The genome was annotated using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) version 2.10 (Tatusova et al, 2016), Rapid Annotation using Subsystem Technology (RAST) version 3.0 (Aziz et al, 2008;Overbeek et al, 2014) and IMG ER pipeline (Markowitz et al, 2009). The genome project and the complete genome sequence were deposited in the Genomes On Line Database (Liolios et al, 2010) and GenBank.…”

Complete genome of Pseudomonas sp. strain L10.10, a psychrotolerant biofertilizer that could promote plant growth

“…Genome annotation was then performed using NCBI Prokaryotic Genome Annotation Pipeline (PGAP) version 2.10 and Rapid Annotation using Subsystem Technology (RAST) version 3.0 (Aziz et al, 2008, Overbeek et al, 2014, Brettin et al, 2015, Xia et al, 2015. The genome of Pseudomonas sp.…”