Home of the SEED

With the growing number of available genomes, the need for an environment to support effective comparative analysis increases. The original SEED Project was started in 2003 by the Fellowship for Interpretation of Genomes (FIG) as a largely unfunded open source effort. Argonne National Laboratory and the University of Chicago joined the project, and now much of the activity occurs at those two institutions (as well as the University of Illinois at Urbana-Champaign, Hope college, San Diego State University, the Burnham Institute and a number of other institutions). The cooperative effort focuses on the development of the comparative genomics environment called the SEED and, more importantly, on the development of curated genomic data.

We provide a SEED-Viewer that allows read-only access to the latest curated data sets. For users interested in editing and learning how to use the system, we provide the Trial-SEED. As described in our manifesto the annotation is not performed on a gene by gene basis per genome, but rather by subsystem by an expert curator across many genomes at a time.

Answering numerous requests for automatic Seed-Quality annotations for more or less complete bacterial and archaeal genomes, we have established the free RAST-Server (RAST=Rapid Annotation using Subsytems Technology). Using similar technology, we make the Metagenomics-RAST-Server freely available.

We make all our software and data available for download and use on our DownloadPage page.

• When using the SEED, please cite: Overbeek et al., Acids Res 33(17), 2005 (Supplementary material)
• Our approaches to annotation, gene calling etc are outlined in a series of Standard Operating Procedures.
• Other papers that use the SEED