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The NMPDR Banner and Search Box

At the top of every page is a banner containing a search box, a graphic logo, and a menu bar. The actual graphic logo used depends on the width of your display and the browser you're using.

The Banners

Examples of both banners are shown below.

banner illustration

As is traditional for modern web sites, clicking in the left-hand portion of the banner graphic will take you to our home page.

The Search Box

The search box works in two modes. When data is selected, you are searching the database for genomic data. When web pages is selected, you are searching the "cover pages" that describe NMPDR and and provide user-support. In other words, if you are looking for a gene, protein, or organism, make sure data is selected (it is by default). If you are looking for more general information about how to use NMPDR or what is NMPDR, then select web pages before submitting your search.

Data Search

With the data option selected, you can type any word or phrase into the search box and click GO to search the Sprout Database. The search box will attempt to find an item that exactly matches what you typed in. If it cannot, it performs a keyword search.

The data search box recognizes the following types of names when searching for an exact match.

  1. An organism number (100226.1, 83333.1) or complete name with strain (Streptomyces coelicolor A3(2), Escherichia coli K12) takes you to the GenomeViewerOrganismPage Organism Overview? page.
  2. A feature's FIGid (fig|243277.1.peg.524, fig|315277.3.peg.412) or a known alias (Q9X8I1_STRCO, P00934), takes you to the Genome Viewer Annotation Page for the specified feature.

Web Pages Search

With the web pages option selected, a Google search is performed of the main NMPDR web site. The search thus performed is very flexible.

  • Searches are not case sensitive. Campylobacter and campylobacter return the same results.
  • Double quotes can be used to form phrases. "Folate biosynthesis" will return fewer pages than Folate biosynthesis without the quotes.
  • A minus sign can be used to exclude terms. So, essential -campylobacter will return pages about essentiality that don't have any reference to Campylobacter.

It's important to understand that the web pages search is a search for text, not a search for features or genomes. Entering virulence -campylobacter will not return a list of virulent genes excluding those found in Campylobacter. Instead, it will find pages that have the word virulence but not the word campylobacter. If you are looking for particular data in the database, you need to select data.

With that said, it is also the case that the data pages are indexed for the web page search. Thus, one of the pages returned for virulence -campylobacter will be fig|282459.1.peg.2618, which is a hypothetically virulent gene in Staphylococcus aureus subsp. aureus MSSA476.

The Menu Bar

Position the mouse cursor over a word to see a dropdown list of menu choices. These are summarized below.

Home
NMPDR Return to the home page for the NMPDR website.
SEED Work with the public version of the SEED Environment for genome annotation.
Annotation Clearinghouse Visit the Annotation Clearinghouse, a web database of assertions about features and protein encoding genes. You can upload your own assertions or view others.
Annotate
RAST Use the Rapid Annotation Server to electronically annotate large Genomes. For more about this service, read our paper at BioMed Central.
MG-RAST Use the Metagenomics Rapid Annotation Server, a variant of the RAST for metagenomes? .
Compare
Annotations Display all the annotations submitted to the Annotation Clearinghouse for a selected genome.
Proteomes Display a table of Bidirectional Best Hits between selected genomes. The table is color-coded so you can visualize the genetic distance between the organisms represented.
Subsystems Compare the metabolic pathways used by two organisms.
Signature Genes Find genes that are common among selected genomes or differentiate two sets of genomes.
FIGfams Find the protein family of a FASTA Format amino acid sequence.
KEGG maps View the KEGG diagrams for a particular genome.
Search
BLAST or Scan Search for protein or DNA sequences using BLAST or our advanced pattern-scanning tool.
Genes Search for genes in selected genomes using keywords, a specific subsystem, or both.
Organisms View a summary of NMPDR core organisms and a list of supporting organisms.
Subsystems View the tree of subsystems, and do keyword searches in individual subsystems or subsystem categories.

Protein Targets Search for genes using a combination of useful criteria.
Batch ID Search Find genes from an uploaded file of IDs.
Index of Search Tools Select one of the Sprout Database search tools.
Resources
Publications See a list of journal papers that reference the NMPDR.
Essential Genes Explore genes determined to be essential in genome-wide screens.
Drug Targets Pipeline Read about our drug target pipeline.
Teaching with NMPDR View presentation materials and student assignments designed to use the NMPDR as a teaching tool.
Downloads Download links for the NMPDR Core Genomes? .
NMPDR Source Code View the documentation of the NMPDR source and access the download links.
Attributions View a list of the tools and data sources used to build the NMPDR.
Cells, Reagents, Databases, Images View links to databases of interest to the bionformatics? community.
Bioinformatics Resource Centers Learn about the BRC project and the web sites that are participating in it.
Regional Centers of Excellence View the ten regional centers established by the Biodefense and Emerging Infectious Diseases Research initiative.
Research Links Search for information on general-interest and bioinformatics web sites.
Help
Where to Start If you're new to the NMPDR, learn how to mine our Sprout Database and read examples of how to use this site to answer biological questions about DNA and proteins.
Glossary Read our glossary of useful terms.
FAQ See our answers to frequently asked questions.
Tutorials and Workshops Learn how to use the NMPDR.
Help Index Go to the home page for all our help materials.
SOPs View our standard operating procedures.
Contact Us View EMAIL and address information about the NMPDR staff.

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Summary About the banner above every page
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Topic attachments
I Attachment Action Size Date Who Comment
pngpng NmpdrBannerExamples.png manage 142.1 K 25 Mar 2009 - 19:15 Leslie Mc Neil  
Topic revision: r38 - 01 Apr 2009 - 20:40:32 - Leslie Mc Neil
 
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.