The subsystem filter is a dropdown menu on a search form that contains a list of subsystem names. It allows you to restrict the output to the features found in a single subsystem. The default is to return all features. That option is indicated by the selection (all). In the example below, the filter has been set to restrict the output to features that participate in the Arginine Biosynthesis subsystem.

Subsystem filter dropdown

Searching for kinase activity in Campylobacter jejuni
The number of features in a single subsystem is very small compared to the total number of features in the system. The screen fragments to the right show two attempts to search for kinase activity in Campylobacter jejuni genomes. An unrestricted search returned 240 results. A subsystem-filtered search returned only 7.

As a result, when you are using the subsystem filter in combination with other search parameters, there is a good possibility that the search will not come back with any results. Subsystem filtering is best used when you know you are searching in the general area of the subsystem's particular metabolic pathway.

If you want to filter on a group of related subsystems, use Sub Search.

Topic revision: r4 - 01 Apr 2009 - 06:30:53 - 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.