SeedViewer Organism - Revision history

Mkubal at 20:16, 7 November 2006

2006-11-07T20:16:21Z

Mkubal at 19:48, 3 November 2006

2006-11-03T19:48:46Z

Mkubal at 19:47, 3 November 2006

2006-11-03T19:47:47Z

Mkubal at 19:46, 3 November 2006

2006-11-03T19:46:01Z

Mkubal at 16:56, 3 November 2006

2006-11-03T16:56:34Z

Mkubal at 16:55, 3 November 2006

2006-11-03T16:55:31Z

Mkubal at 16:55, 3 November 2006

2006-11-03T16:55:04Z

Mkubal at 16:54, 3 November 2006

2006-11-03T16:54:20Z

Mkubal at 15:58, 3 November 2006

2006-11-03T15:58:39Z

New page

Organism Page in SEED Viewer

In the green bar at the top of the page adjacent to the homepage symbol is 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

View Features

View Reactions

@@ Line 6: / Line 6: @@
 Overview
 :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 PEGs with hypothetical and non-hypothetical function assignments is provided in box in the top right corner of the page.<br>
+: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.
-: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.<br>
+: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>
 :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 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.
@@ Line 20: / Line 20: @@
 :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>
-: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.<br>
+: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.
 :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>

@@ Line 27: / Line 27: @@
 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>
 :The total number of features for this genome is displayed above the table.<br>

@@ Line 28: / Line 28: @@
 View Features
 :Selecting this display provides a table containing feature ID, functional assignment, starting and stopping location in 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>
 :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 clicking enter.
+: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

← Older revision		Revision as of 19:46, 3 November 2006
Line 27:		Line 27:

	View Features		View Features
		+	:Selecting this display provides a table containing feature ID, functional assignment, starting and stopping location in base pairs relative<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>
		+	: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 clicking 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		View Reactions

@@ Line 15: / Line 15: @@
 Browse Genome
-:This display allows a you to walk the chromosome of the selected genome.<br>
+: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.
 :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>

@@ Line 1: / Line 1: @@
 Organism Page in SEED Viewer
-In the green bar at the top of the page adjacent to the homepage symbol is pulldown menu<br>
+In the green bar at the top of the page adjacent to the homepage symbol is a pulldown menu<br>
 labeled 'This Organism' with the following 4 display options for this page:<br>