The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). 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.  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/).  If the genome is made public, it is then housed within the SEED and its proteins populate the FIGfam collection.  Here we describe the interconnectedness of the SEED database and RAST, the RAST annotation pipeline and updates to both resources.
SEED
The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). 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.  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.
RAST