Search the NMPDR Database
Keyword Search: Type one or more keywords into the box and click go. Keywords can include gene IDs (
gi|14247351), gene names (dnaK), EC numbers (2.7.6.3), genus (Vibrio), species (vulnificus), and words contained in subsystem names (transport), functional assignments (phosphoglycerate), and subsystem classes (membrane). You may also use attributes like iedb, virulence, and essential. A list of protein encoding genes that match all of the keywords will be returned.
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To search for genes matching only some of the keywords, surround the optional words with parentheses. For example,
2.7.6.3 4.1.2.25 would match all bifunctional genes associated with both EC numbers 2.7.6.3 and 4.1.2.25, while (2.7.6.3) (4.1.2.25) would match the bifunctional genes as well as all single function genes with either of those EC numbers. Use a minus sign to exclude genes matching a particular keyword. For example, Vibrio -hypothetical would match all Vibrio genes except those marked hypothetical.
Finally, you can use quotes to ensure the keywords appear in the proper order. For example, a search of Campylobacter coli RM2228 for membrane protein will match all genes with the words membrane and protein anywhere in the annotation. In particular, it will match fig|306254.1.peg.102 Ankyrin repeat-containing possible periplasmic protein, which has a cellular localization prediction of "outer membrane". To exclude this gene and others like it, you would instead search for "membrane protein", which will only match genes that encode actual membrane proteins.
Other Search Links
- Full Search: Go to the Gene Search page to compose an advanced query with limits on Genomes or Subsystems.
- BLAST or Scan: Go to the Tool Search page to search using a DNA or amino acid sequence as the query term. The sequence may be an exact gene or protein sequence (BLAST) or a degenerate motif (Scan).
- Subsystems: Go to the Subsystem Search page to select a subsystem for browsing from a hierarchical list or to search for a gene within a chosen subsystem.
- Organisms: Go to the Organism Data Summaries page to see the annotation status of any organism in the database.
Topic revision: r4 - 26 Aug 2008 - 12:47:21 - BruceParrello
NMPDR is 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.