The Subsystems Approach to Genome Annotation

The subsystems approach to genome annotation is the primary route by which the functional roles of genes are assigned in the NMPDR.

A subsystem is a set of proteins that perform related functional roles. Roles can be steps in a single metabolic pathway, such as histidine degradation, or components of a cellular structure, such as Ribosome SSU bacterial.

Subsystems allow the annotator to work vertically through similar systems in many genomes (blue arrow in diagram), rather than horizontally through a single genome (green arrow in diagram). The subsystem curator rapidly develops expertise in the variations of the subsystem in different organisms, and this enables faster, more accurate annotations. Curators work in a private installation of the editable annotation environment, SEED, which is also available in a public installation for those who would like to create a subsystem that captures their expertise and knowledge of a set of proteins.

Browse or search subsystems

The Subsystems tree allows you to browse our entire set of curated subsystems, or to restrict a protein/gene search to a subsystem selected from the tree (accessible from the Search menu).

Further Reading:

Topic revision: r10 - 03 Apr 2009 - 14:40:18 - TWiki Guest
Notice to NMPDR Users - The NMPDR BRC contract has ended and bacterial data from NMPDR has been transferred to PATRIC (, 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.