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At the top of every page is a banner containing a search box, a graphic logo, and a navigation 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.

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, it takes you to a page in the GenomeViewer. When web pages is selected, it performs a text search of the entire web site.

Data Search

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

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

1. An organism taxon number (100226.1, 83333.1) or name (Streptomyces coelicolor A3(2), Escherichia coli K12) takes you to the specified organism's GenomeViewer OrganismPage? .
2. A Contig? ID (83333.1:NC_000913, nmpdr|100226.1.contig.NC_003904, will take you to the GenomeViewer's ContigViewPage? for that contig.
3. A feature's FigId (fig|100226.1.peg.3361, fig|83333.1.peg.4) or a known FeatureName? (Q9X8I1_STRCO, P00934), takes you to the GenomeViewer AnnotationPage? 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 essential 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 in the GenomeViewer 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 virulent.

The Navigation Bar

The navigation bar works like a standard menu. Position the mouse cursor over a word to see a dropdown list of menu choices. These are summarized below.

Navigate
Home		Main entry page
Search		Search page. Perform a direct KeywordBox search of the data and learn about NMPDR searching.
NMPDR Organisms		See annotation summaries for the NMPDR CoreOrganisms, and link to GenomeViewer pages for the other organisms in the SproutDatabase.
Genome Viewer		Go to the GenomeViewer to search, view, and analyze our genomic data.
Drug, Antitoxin, Vaccine Targets		Read about our efforts to identify drug targets and compute docking energies.
Essential Genes		View a graph of essential genes identified by selected journal papers.
NMPDR Downloads		View and download GFF, XML, and FastaFormat files for the NMPDR CoreOrganisms.
Services
Rapid Annotation Using Subsystem Technology		Use the RapidAnnotationServer to electronically annotate large Genomes. For more about this service, read our paper at BioMed Central.
Meta Genome - RAST		The MetagenomicsRapidAnnotationServer uses a variation of the standard RAST algorithms to electronically annotate Metagenomes? .
Annotation Clearinghouse		The AnnotationClearinghouse is a web database of assertions about features and protein encoding genes. You can upload your own assertions or view others.
Comparative Tools
Annotation Clearinghouse Comparison		Display all the annotations submitted to the AnnotationClearinghouse for a selected genome.
Homolog Spreadsheet Tool		The HomologSpreadsheet? displays a table of BidrectionalBestHits? between selected genomes. The table is color-coded so you can visualize the genetic distance between the organisms represented.
Signature Genes Tool		The SigGenes tool allows you to search for features that are common between genomes or that distinguish two groups of genomes from one another.
News
New Developments		View articles about recent changes to the NMPDR web site.
Counts and Statistics		See a monthly summary of what we have in our database and on the site.
News and Journals		Links to articles about the NMPDR website and to online peer-reviewed journals.
Conference Calendar		A calendar covering events of interest to NMPDR users.
Publications		Links to presentations and publications about the NMPDR and our suite of bioinformatics? tools.
External Links
Cells Reagents Databases Images		Links to databases of interest to the bioinformatics? community
Bioinformatics Resource Centers		A description of the BRC project and links to the other websites that are participating in it.
Regional Centers of Excellence		A list of the ten regional centers established by the Biodefense and Emerging Infectious Diseases Research initiative, with links.
About Us
NMPDR		A description of the NMPDR project.
The SEED		A description of the SEED, the tool used to create and curate the data in the SproutDatabase, along with a link to the original SEED paper.
Contact Us		Our mailing address, email links, and forms to sign up for our mailing lists.
Help
Where to Start		Instructions on how to find genes using the NMPDR, plus links to examples of using the NMPDR to answer biological questions.
FAQs		Frequently asked questions.
Help Pages		Pages describing the NMPDR and how to use it.
Tutorials		Links to the NMPDR tutorial pages.
Teaching Materials		Instructions on how to use the NMPDR for teaching bioinformatics? concepts.
Citing NMPDR		How to reference NMPDR in bibliographies and attribution lists.
Standard Operating Procedures		Our procedures for managing, maintaining, and using the NMPDR web site.
Sprout Database		Diagram of our database, with detailed explanation of the data.
Research Central		Live search forms for finding useful information in various places around the web.