The SEED

The SEED is the foundation of the NMPDR project. The public SEED at the University of Chicago can be used to edit the functional annotations of genes or to create a subsystem that describes your work. The SEED includes viral and environmental genomes, as well as incomplete genomes that are not available in NMPDR. The system is presently undergoing a complete makeover, which you can see at the new home of the seed.

The tutorial, "Annotating Proteins and Adding Proteins to Subsystems—A Worked, Eukaryotic Example," describes the steps taken to exchange a meaningless protein name (syntenic homolog of YCL030C) with a functional annotation. The re-named protein is then added to a subsystem that describes histidine biosynthesis. A protein from the filamentous fungus Eremothecium gossypii is used as the example because NMPDR annotators work quickly to provide meaningful, functional annotations to bacterial genomes, so any bacterial examples immediately become obsolete. The workflow described for annotating genes and creating subsystems is the same for bacterial genomes. From within the SEED environment, other tutorials on annotation may be found by following the SEED Wiki link the blue SEED header.

The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes.
Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, Cohoon M, de Crecy-Lagard V, Diaz N, Disz T, Edwards R, Fonstein M, Frank ED, Gerdes S, Glass EM, Goesmann A, Hanson A, Iwata-Reuyl D, Jensen R, Jamshidi N, Krause L, Kubal M, Larsen N, Linke B, McHardy AC, Meyer F, Neuweger H, Olsen G, Olson R, Osterman A, Portnoy V, Pusch GD, Rodionov DA, Ruckert C, Steiner J, Stevens R, Thiele I, Vassieva O, Ye Y, Zagnitko O, Vonstein V.

Nucleic Acids Res. 2005 Oct 7;33(17):5691-702.    PMID: 16214803

In this paper, subsystems are defined, and the SEED annotation environment that supports the creation, curation, population and exchange of subsystems is described. The SEED is used by the NMPDR curation staff, and a public version is available for community annotation.