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 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, Mc Hardy? 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 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.
SequencingForm
Sequence 000500
Summary The annotation software used by the NMPDR Genome Pipeline
Topic revision: r6 - 12 Oct 2008 - 00:00:05 - TWiki Guest
 
Notice to NMPDR Users - The NMPDR BRC contract has ended and bacterial data from NMPDR has been transferred to PATRIC (http://www.patricbrc.org), a new consolidated BRC for all NIAID category A-C priority pathogenic bacteria. NMPDR was a collaboration among researchers from the Computation Institute of the University of Chicago, the Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, and the National Center for Supercomputing Applications (NCSA) at the University of Illinois. NMPDR is funded by the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, under Contract HHSN266200400042C. Banner images are copyright © Dennis Kunkel.