The SEED

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Contents 1 Database Description 2 Research 3 Authors 4 External Links

[edit] Database Description

The SEED is a fully integrative microbial genome annotation, analysis, metabolic reconstruction, and interrogation platform that integrates annotations from all known microbial genome and metagenome sources into a single comprehensive database for comparative genomics.

[edit] Research

The currently available database contains over 750 complete microbial genomes, most of which have been reannotated by the team of experts. The SEED database was the first resource to provide vertical annotations across many genomes. The old process of annotating one-gene, one-genome at a time does not scale to the thousands of genomes that are expected to be sequenced over the next few years.

This revolution in annotation technique resulted in several new paradigms. The FIGfams, protein families developed from sets of conserved proteins are providing a resource for comparative annotations. The scenarios, developed as a plug-in by Aaron Best, Matt DeJongh and colleagues at Hope College provide a mechanism for automation of the metabolic reconstruction from genomes.

The SEED developers have created two unique services that allow end users to upload raw sequences for automatic, high-quality annotation

• The RAST Server for complete genome annotation
• The mg-RAST Server for metagenome annotation

Research continues on these, and other exciting areas of microbial genomics, using The SEED database.

[edit] Authors

The SEED was written by Ross Overbeek and collaborators at FIG. Much of the interface development was by members of Argonne National Laboratory.

[edit] External Links

The SEED