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 home page provides a current total and complete count of each type.
Click on archael, bacterial, eukaryal, or viral to display a table listing the genomes in this set.

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 the 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.

The search will treat the entered text as a regular expression and match strings and substrings found in functional roles, subsystems and features.

The results of the search will be displayed in up to 4 tables, a Functional Role table, Subsystem table,Features table and Organisms table.

If a search returns only a single match, the appropriate SEED Viewer page will be displayed and the intermediate search results page with the tables

mentioned above will not be displayed.

The number of hits associated with a functional role will appear above the Functional Role table.

The number of features returned is limited to 100.

To browse the results quickly use the next >> and last >> links.

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

If you check the 'quick search' option, the results will be limited to functionals role in a subsystem.

In any of the results tables,

clicking on a functional role will take you to a Functional Role page in the SEED Viewer,

clicking on a subsystem will take you to a Subsystem page in the SEED Viewer and

clicking on a feature ID will take you an Annotation page in the SEED Viewer.

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.