Difference between revisions of "SeedViewer Organism"
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Browse Genome | Browse Genome | ||
| − | :This display allows | + | :This display allows you to walk the chromosome of the selected genome.<br> |
:If the genome is not completely assembled, the first contig will be selected. | :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.<br> | :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.<br> | ||
Revision as of 10:56, 3 November 2006
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.
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