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Help: Instructions and Examples

Instructions

Where do I Start?

Start with a keyword search for the name of a gene or protein from the search box in the header. Click the "Search" option in the Navigate menu for more ways to SearchNMPDR.

Start with the nucleotide sequence of your gene or the amino acid sequence of your protein and use the BlastSearch against any complete genome. You can specify multiple genomes, but of course searching more genomes takes more time.

Start from the annotation status table of an OrganismDataSummaries page, such as the Staphylococcus page, which provides quick access to proteins about which much is known (named genes in subsystems), little is known (named genes not in subsystems and hypothetical genes in subsystems), or nothing is known (hypothetical genes not in subsystems).

Start from the subsystems tree to view the phylogenetic distribution of an interesting biological process.

Use the NmpdrBanner to navigate the site.

For a thorough demonstration of the many ways to find your gene of interest, see the tutorial, Find.

What Do I Do?

View the protein you found in the context of its chromosomal region and in comparison with four closely related genomes by clicking the Viewer button in the search results table.

Expand the comparison using regular or advanced display options, then update the graphic.

Explore the biological context of the protein you found by clicking a subsystem link (if present) from the search results table, the annotation overview page (viewer), or by selecting a subsystem from the subsystems tree.

Browse all features in a genome by selecting an organism and then following the Genome Browser link. Information is displayed in a graphic as well as a table that will focus the image.

How do I Save or Download Data?

To save the table of SearchResults as a tab-delimited text file that may be opened as a spreadsheet, simply click on the download button. This will save all results, not just those currently displayed. You may also download all amino acid or nucleotide sequences of the search results with one-click buttons.

To save individual protein or gene sequences from a protein page, use the sequence link next to the FigId to go to display the desired sequence in FastaFormat, which you can copy and paste into a local file.

Examples

These pages contain examples of how the NMPDR can be used to answer biological questions.

• SOP031: Finding a Degenerate Peptide Motif in Selected Organisms
• SOP033: Finding Genes that are Important in Specific Types of Pathogens
• SOP032: Finding Genes that May Be Characteristics of a Phenotype