Help: Instructions and Examples

Instructions
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 Search NMPDR.

Start with the nucleotide sequence of your gene or the amino acid sequence of your protein and use the BLAST Search 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 Organism Data Summaries 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 NMPDR banner 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 results table.

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

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.

download buttons shown on search results page

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

SequencingForm
Sequence
Summary	Where to start and what to do, plus links to examples

Attachments

Topic attachments
I	Attachment	Action	Size	Date	Who
png	browsegenome.png	manage	87.0 K	03 Dec 2008 - 00:15	Leslie Mc Neil
png	displayoptions.png	manage	48.6 K	03 Dec 2008 - 00:16	Leslie Mc Neil
png	visualcompare.png	manage	56.6 K	03 Dec 2008 - 00:16	Leslie Mc Neil

Topic revision: r7 - 03 Feb 2009 - 23:59:14 - Bruce Parrello

NMPDR is 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.