National Microbial Pathogen Data Resource

Begin by entering keywords in the box above to search all publicly available, essentially complete genomes for a gene or protein to work on. Keywords may be any alphanumeric label, including Enzyme Commission (EC) numbers or accession numbers assigned by other data resources such as GenBank and SwissProt. Multiple search terms will automatically be joined with "AND." Try, for example, "vibrio toxin."

• Limit the search to your focus group of orgamisms by starting on an organism summary page, linked at left, or clicking the Genes link for more options.

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

Continue from the table of text or BLAST search results, which will allow you to examine your protein in the GBrowse or NMPDR environment. Click the NMPDR button to view your protein (highlighted green) in the context of its neighbors in close proximity on the genome and to compare this region with homologous regions in other genomes.

Context of your protein on the genome is presented in a graphic and in a table that provides the functional annotations of genes within about 8 kb up- and downstream of your focus gene.

Functional Clusters that include your protein (highlighted green) are represented as blue arrows in the context graphic. In the context table, proximal genes that are functionally clustered with the focus gene will have a score, fc-sc. The score is approximately equal to the number of different species (not strains) in which the two genes are co-localized. Clusters in other genomes and a table of homologous pairs are returned by clicking the CL button or the fc-sc, respectively.

Compare your protein with homologous regions in the maximum number of other genomes by clicking the Pins button in the context table. A subset of the pins display, initially limited to 5 genomes that share the most similar proteins in this region, is returned by clicking "Show Compare Regions." The size of the chromosomal region and number of genomes displayed may be reset by the user.

Align your protein with others you select from a table orthologs identified by a pre-calculated, reciprocal BLAST analysis by clicking the button, "Bidirectional Best Hits."

Sequence of the protein and DNA are provided in FASTA format. Flanking sequence of 500 nucleotides up- and downstream of the gene are also readily available.

Instructions are avaliable in the list of frequently asked questions, or the tutorials, Searching NMPDR and Navigating NMPDR, which are also online at NCSA.