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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.

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.

What Do I Do?

Limit the search to your focus group of organisms by including the taxonomic name in the search, starting on one of the OrganismDataSummaries pages, or using the advanced search? .

BLAST your protein or gene sequence from the BLAST or Scan link.

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