SeedViewer Organism

Organism Page in SEED Viewer

In the green bar at the top of the page adjacent to the homepage symbol is a pulldown menu
labeled 'This Organism' with the following 4 display options for this page:

Overview

The top of page provides summary statistics for this genome including the numbers of subsystems, coding sequences, RNAs and other background information.

A breakdown of the number of PEGs with hypothetical and non-hypothetical function assignments is provided in box in the top right corner of the page.

Adjacent to the Taxonomy ID is the Wikipedia Globe that is linked to the Wikipedia entry for this organism.

On the bottom left of the page a bar graph depicts the percentages of PEGs for this genome that are present in at least one subsystem.

Next to the bar graph a pie chart and accompanying expandable hierarchical tree, color coded to match the pie chart, organizes the subsystems

present in this genome by cellular process.

At every level in the tree the number of PEGs in each category is listed in parentheses.

At the leaves of the tree are links to a Subsytem page in the SEED Viewer.

Browse Genome

This display allows you to walk the chromosome of the selected genome.

If the genome is not completely assembled, the first contig will be selected.

The window size in terms of number of base pairs can be selected using the 'Window Size' pulldown menu, or the 'zoom in' or 'zoom out' buttons.

The < and > buttons will move the window down or up the chromosome half the window size.

The << and >> buttons will move the window down or up the chromosome a full window size.

Under 'Options' you can select which features are displayed and the number of reading frames. By default the genome browser offers a two frame view of the currently selected organism.

After selecting your options, click the 'Refresh' button to update the page.

On the middle line of the chromosome display you will see features not associated with a reading frame, such as rnas, pathogenicity islands or prophages.

Hover over a feature in the chromosome display for a detailed description.

Clicking an item will take you to the Annotation page in the SEED Viewer for this feature.

View Features

Selecting this display provides a table containing feature ID, functional assignment, starting and stopping location in terms of base pairs relative

to the beginning of the contig, feature type and a list of aliases.

The total number of features for this genome is displayed above the table.

Use the 'next>>' and 'last>>' links to quickly scroll through sets of 10 features.

Filter features across the entire genome by using the text entry boxes in the 'Functional Assignment', 'Type' or 'Aliases' column header and then hitting enter.

Sort or reverse sort the tables using the triangle in the columns headers.

Export all or a subset of the features, after filtering, of a genome to a spreadsheet file using the 'Export Table' button.

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