NMPDR> FIG Web>NmpdrSearch  

The NMPDR search facility provides many different ways to look for genes, genomes, or sequences? in the NMPDR database. The following searches are currently supported.

• DrugSearch 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 ...
• GeneSearch 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 ...
• OpSearch 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 ...
• SigGenes 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 ...
• SubSearch 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 below ...
• ToolSearch The sequence search is designed to locate matching DNA or protein sequences among selected genomes in the NMPDR database. It includes three BLAST tools and two ...
• WordSearch The Word Search is a bare bones search tool that searches all of the genomes in the NMPDR database using keywords entered in a KeywordBox. The standard GeneDisplayOptions ...

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.

Most NMPDR searches use a powerful GenomeControl that allows you to choose one or more genomes according to various criteria. Some also use a search-engine style KeywordBox. 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.

• GeneDisplayOptions The gene display options control the display of genes in the NMPDR Search Results . /GeneDisplayOptions.png If Sort by Function is checked, the search output ...
• GenomeControl 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 ...
• IdentifierType 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 ...
• KeywordBox 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 ...
• SubsystemFilter 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, mouse over the a question mark to get a hint. Click on the blue question mark to pop up the Wiki page on the subject. The blue question marks have been circled in the sample search form below.