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Search the NMPDR Database

Quick search

Keyword Search Read more Click to hide help
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 genes that match all of the keywords will be returned.

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.

Forms for advanced or specialized searches

The NMPDR search facility provides many different ways to look for genes or sequences in the Sprout Database. The following searches are currently supported.

  • Batch Search The Batch Search is not technically a search in the normal sense; rather, it allows you to upload a list of feature IDs and see them as SearchResults. The IDs ...
  • Drug Search One of the projects underway at the NMPDR is generating in silico docking results for proteins that are believed to be good drug targets. For each selected protein ...
  • Gene BBH Search The Gene BBH Search is a simple tool that lists all the BidirectionalBestHits of a particular gene . Simply enter the gene's name (usually a FigId or alias ...
  • Gene Search The gene search allows you to search for features in a specific set of organisms. Use the GenomeControl to select the organisms you want to search. Specify search ...
  • Op Search The operon search displays features from a single genome in operon order . Features that are reasonably close to each other on the same strand are displayed ...
  • Org Sum Search Organism Summary Search The organism summary search is a simple search tool that displays genes in a single genome organized according to how confident we ...
  • Sig Genes Use the signature genes tool to find genes that are common among one set of genomes , or differentiate one set from another. Like most searches in the NMPDR ...
  • Sub Search Subsystems are organized in broad functional categories. The subsystem search tool displays the subsystems and their categories in the form of a tree, as shown on ...
  • Target Search Protein Target Search Introduction The protein target search allows you to search for features using a boolean combination of various criteria. You can find the ...
  • Sequence Search Sequence Search The sequence search is designed to locate matching DNA or protein sequences among selected genomes in the NMPDR database. It includes three BLAST ...
  • Word Search Keyword Search The Keyword Search is a bare bones search tool that searches all of the genomes in the NMPDR database using keywords you enter in a standard keyword ...

The search results will generally start with data for the NMPDR core organisms. All NMPDR searches allow you to download results in tab-delimited and XML formats. NMPDR searches that return a list of genes also allow you to download the genes in FASTA format or view them in an interactive table.

Most NMPDR searches use a powerful Genome Control that allows you to choose one or more genomes according to various criteria. Some also use a search-engine style Keyword Box. The Keyword Box can also be found at the top of many of the NMPDR pages. The pages listed below describe these and other search controls.

  • Gene Display Options The gene display options control the display of genes in the NMPDR Search Results . If Sort by Function is checked, the search output will be sorted by ...
  • Genome Control The Genome Control is a powerful tool for selecting one or more genomes . It lists every genome available in the NMPDR. The NMPDR core organisms are shown first ...
  • Identifier Type In each search form, the Identifier Type dropdown box, shown below, can be used to determine how feature IDs will be displayed in the search results. Normally ...
  • Keyword Box The NMPDR keyword search works like a typical search engine. You type in the appropriate words, and a list of genes will come back. Our keyword database contains millions ...
  • Subsystem Filter 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 ...

If you have a question about something in an NMPDR search form, click the tiny help link get a hint. The help links have been circled in the sample search form below.

Topic revision: r17 - 01 Apr 2009 - 03:54:29 - Bruce Parrello
 
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.