SeedViewer Home

Counts of Genomes in the SEED

The SEED contains archeal, bacterial, eukaryal, and viral genomes, as well as environmental samples.
A box on the top right of the page provides a current total and complete count of each type.

Searching

The SEED Viewer's home page provides 4 different perspectives on searching to help you effciently access the data in the SEED.
By clicking on 'Text Search','BLAST Search', 'Subsystems' or 'Organisms' you can change your search perspective.
Notice that the text on button to the right of the text entry box will change after clicking on one of these perspectives.

Text Search

This is the default search option. Enter a key word or phrase in the text box and click the 'Text Search' button to the right of the text box.

This search cover features, functional roles and subsystems.

If you check the 'quick search' option, the results will be limited to features associated with a functional role in a subsystem.

The results of the search will be displayed in 2 tables, a Functional Role table and Subsystem table. The number of hits associated

with a functional role will appear above the Functional Role table. To browse the results quickly use the next >> and last >> links.

The columns in both tables can be alphanumerically sorted and reverse sorted by clicking on the respective triangle in the column header.

Blast Search

Enter a DNA or amino acid sequence, and select a genome from the pulldown menu above the text box. You must select a genome.

Then click the 'Blast Search' button to the right of the genome pulldown menu.

The results will be in typical Blast output format and include PEG IDs that are linked to an Annotation page in the SEED Viewer.

Subsystems Search

Selecting this option provides an alphanumerically sorted pulldown menu of subsystems in the SEED and also a text entry box.

Notice as you type in text entry box the pulldown menu is automatically updated with subsystems that contain the entered text,

and not just matching at the beginning of the subsystem name.

After selecting a subsystem, clicking the 'View Subsystem' button will take you a Subsystem page in the SEED Viewer.

Organism Search

Selecting this option provides an alphabetized pulldown menu of genomes in the SEED and also a text entry box.

Notice as you type in text entry box the pulldown menu is automatically updated with genomes that contain the entered text,

and not just matching at the beginning of the genome.

After selecting an organism, clicking the 'View Organism' button will take you an organism page in the SEED Viewer.