Difference between revisions of "SeedViewer Organism"
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Overview | Overview | ||
:The top of page provides summary statistics for this genome including the numbers of subsystems, coding sequences, RNAs and other background information.<br> | :The top of page provides summary statistics for this genome including the numbers of subsystems, coding sequences, RNAs and other background information.<br> | ||
| − | :A breakdown of the number of | + | :A breakdown of the number of protein encoding genes with hypothetical and non-hypothetical function assignments is provided in box in the top right corner of the page.<br> |
:Adjacent to the Taxonomy ID is the Wikipedia Globe that is linked to the Wikipedia entry for this organism. | :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 | + | :On the bottom left of the page a bar graph depicts the percentages of protein encoding genes for this genome that are present in at least one subsystem.<br> |
:Next to the bar graph a pie chart and accompanying expandable hierarchical tree, color coded to match the pie chart, organizes the subsystems<br> | :Next to the bar graph a pie chart and accompanying expandable hierarchical tree, color coded to match the pie chart, organizes the subsystems<br> | ||
:present in this genome by cellular process. | :present in this genome by cellular process. | ||
| − | :At every level in the tree the number of | + | :At every level in the tree the number of protein encoding genes in each category is listed in parentheses. |
:At the leaves of the tree are links to a Subsytem page in the SEED Viewer. | :At the leaves of the tree are links to a Subsytem page in the SEED Viewer. | ||
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:The < and > buttons will move the window down or up the chromosome half the window size.<br> | :The < and > buttons will move the window down or up the chromosome half the window size.<br> | ||
:The << and >> buttons will move the window down or up the chromosome a full window size.<br> | :The << and >> buttons will move the window down or up the chromosome a full window size.<br> | ||
| − | :Under 'Options' you can select which features | + | :Under 'Options' you can select which features and the number of strands or reading frames displayed. By default the genome browser offers a two strand view of the currently selected organism.<br> |
:After selecting your options, click the 'Refresh' button to update the page. | :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.<br> | :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.<br> | ||
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View Features | View Features | ||
| − | :Selecting this display provides a table containing feature ID, functional assignment, starting and stopping location in base pairs relative<br> | + | :Selecting this display provides a table containing feature ID, functional assignment, starting and stopping location in terms of base pairs relative<br> |
| − | to the beginning of the contig, feature type and a list of aliases.<br> | + | :to the beginning of the contig, feature type and a list of aliases.<br> |
:The total number of features for this genome is displayed above the table.<br> | :The total number of features for this genome is displayed above the table.<br> | ||
:Use the 'next>>' and 'last>>' links to quickly scroll through sets of 10 features.<br> | :Use the 'next>>' and 'last>>' links to quickly scroll through sets of 10 features.<br> | ||
| − | :Filter features across the entire genome by using the text entry boxes in the 'Functional Assignment', 'Type' or 'Aliases' column header and then | + | :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. | :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. | :Export all or a subset of the features, after filtering, of a genome to a spreadsheet file using the 'Export Table' button. | ||
View Reactions | View Reactions | ||
Latest revision as of 15:16, 7 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 protein encoding genes 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 protein encoding genes 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 protein encoding genes 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 and the number of strands or reading frames displayed. By default the genome browser offers a two strand 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.
View Reactions