GenDBWiki/WebDocumentation/MainViews/ContigView - Revision history

Agoesman at 15:17, 10 November 2011

2011-11-10T15:17:32Z

← Older revision		Revision as of 17:17, 10 November 2011
Line 2:		Line 2:
	= The GenDB web Contig View =		= The GenDB web Contig View =

	[[~~Image~~:~~GenDBWiki$$WebDocumentation$$MainViews$$ContigView$~~GenDB22bMain.png]]		[[File:GenDB22bMain.png\|GenDB Main Window]]

	{\| border="1" cellpadding="2" cellspacing="0"		{\| border="1" cellpadding="2" cellspacing="0"
	\| '''1'''		\| '''1'''
	\| Menu Bar		\| Menu Bar
	\| The menu bar on top of the window is the main navigation bar for the GenDB web interface.		\| The menu bar on top of the window is the main navigation bar for the GenDB web interface.
	\|-		\|-
	\|colspan="2" \|		\|colspan="2" \|
	\| ''Contig'' shows you a list of available contigs in this project. This list is ordered by ascending length of the contigs.		\| ''Contig'' shows you a list of available contigs in this project. This list is ordered by ascending length of the contigs.
	\|-		\|-
	\|colspan="2" \|		\|colspan="2" \|
	\| ''Tools'' consist currently of to tools. One is the circular plot to view the genome as a circle and the second is PatScan which can search for patterns in a sequence		\| ''Tools'' consist currently of to tools. One is the circular plot to view the genome as a circle and the second is PatScan which can search for patterns in a sequence
	\|-		\|-
	\|colspan="2" \|		\|colspan="2" \|
	\| With ''Classification'' you can choose between three common classification systems namely GO, KEGG and COG		\| With ''Classification'' you can choose between three common classification systems namely GO, KEGG and COG
	\|-		\|-
	\|colspan="2" \|		\|colspan="2" \|
	\| ''Preferences'' has a submenu to call the preferences dialog and an option to view/hide the region observations in the ''Contig View''		\| ''Preferences'' has a submenu to call the preferences dialog and an option to view/hide the region observations in the ''Contig View''
	\|-		\|-
	\| '''2'''		\| '''2'''
	\| Contig View		\| Contig View
	\| The ''Contig View'' displays all visible regions of the selected contig. The visibility and colors can be adjusted in the preferences		\| The ''Contig View'' displays all visible regions of the selected contig. The visibility and colors can be adjusted in the preferences
	\|-		\|-
	\| '''3'''		\| '''3'''
	\| Plot View		\| Plot View
	\| The ''Plot View'' can display the GC-Plot, GC-Skew and the Frame-Plot. Each plot can be toggled with a click on its appropriate box in the legend		\| The ''Plot View'' can display the GC-Plot, GC-Skew and the Frame-Plot. Each plot can be toggled with a click on its appropriate box in the legend
	\|-		\|-
	\| '''4'''		\| '''4'''
	\| QuickNav Bar		\| QuickNav Bar
	\| The ''Quick Navigation Bar'' is used to easily jump to specific parts of the contig while displaying the current position with the red box. Simply click to move the red box		\| The ''Quick Navigation Bar'' is used to easily jump to specific parts of the contig while displaying the current position with the red box. Simply click to move the red box
	\|-		\|-
	\| '''5'''		\| '''5'''
	\| Region Info		\| Region Info
	\| This part shows all informations about the currently selected region. These are categorized in 3 categories: Region info, Annotation Region and Annotation Function		\| This part shows all informations about the currently selected region. These are categorized in 3 categories: Region info, Annotation Region and Annotation Function
	\|-		\|-
	\| '''6'''		\| '''6'''
	\| Contig Info		\| Contig Info
	\| This part summarizes some statistics of the selected contig		\| This part summarizes some statistics of the selected contig
	\|-		\|-
	\| '''7'''		\| '''7'''
	\| Action View		\| Action View
	\| This view replaces the right mouse button of the GenDB-GUI. All the actions from the ''right-click-menu'' moved to here		\| This view replaces the right mouse button of the GenDB-GUI. All the actions from the ''right-click-menu'' moved to here
	\|-		\|-
	\| '''8'''		\| '''8'''
	\| Navigation		\| Navigation
	\| With the arrows at the upper right/left corner you can navigate up-/downstream the contig		\| With the arrows at the upper right/left corner you can navigate up-/downstream the contig

Admin: 5 revisions

2011-10-26T06:17:05Z

5 revisions

← Older revision	Revision as of 08:17, 26 October 2011
(No difference)

imported>AlexanderGoesmann at 15:50, 25 August 2005

2005-08-25T15:50:47Z

← Older revision		Revision as of 17:50, 25 August 2005
Line 13:		Line 13:
	\|-		\|-
	\|colspan="2" \|		\|colspan="2" \|
	\| ''Tools'' consist currently of to tools. One is the circular plot to view the genome as a circle and the second is [[PatScan]] which can search for patterns in a sequence		\| ''Tools'' consist currently of to tools. One is the circular plot to view the genome as a circle and the second is PatScan which can search for patterns in a sequence
	\|-		\|-
	\|colspan="2" \|		\|colspan="2" \|

imported>AlexanderLenhardt at 14:31, 26 November 2004

2004-11-26T14:31:27Z

← Older revision		Revision as of 16:31, 26 November 2004
Line 2:		Line 2:
	= The GenDB web Contig View =		= The GenDB web Contig View =

	[[Image:GenDBWiki$$WebDocumentation$$MainViews$$ContigView$~~GenDB22Main~~.png]]		[[Image:GenDBWiki$$WebDocumentation$$MainViews$$ContigView$GenDB22bMain.png]]

	{\| border="1" cellpadding="2" cellspacing="0"		{\| border="1" cellpadding="2" cellspacing="0"
	\| Menu Bar		\| '''1'''
			\| Menu Bar
	\| The menu bar on top of the window is the main navigation bar for the GenDB web interface.		\| The menu bar on top of the window is the main navigation bar for the GenDB web interface.
	\|-		\|-
	\| ~~Contig Selection~~		\|colspan="2" \|
	\| ~~Shows~~ a list of contigs in ~~the~~ project. ~~In addition the contig~~ length, the ~~number of regions in various states is listed~~.		\| ''Contig'' shows you a list of available contigs in this project. This list is ordered by ascending length of the contigs.
	\|-		\|-
	\| ~~Contig View~~		\|colspan="2" \|
	\| ~~Shows an overview~~ of ~~regions in~~ the for ~~the currently selected contig.~~		\| ''Tools'' consist currently of to tools. One is the circular plot to view the genome as a circle and the second is [[PatScan]] which can search for patterns in a sequence
	\|-		\|-
	\| ~~GC plot~~		\|colspan="2" \|
	\| ~~This window shows a GC~~ and ~~GC-skew plot for the part of sequence currently shown in the Contig View.~~		\| With ''Classification'' you can choose between three common classification systems namely GO, KEGG and COG
	\|-		\|-
	\| ~~Quick navigation bar~~		\|colspan="2" \|
	\| ~~Clicking here moves~~ the ~~Contig View~~ to the ~~part of genome~~ the ~~user clicked. When multiple regions have been selected these are also shown here as ticks on the contig.~~		\| ''Preferences'' has a submenu to call the preferences dialog and an option to view/hide the region observations in the ''Contig View''
	\|-		\|-
	\| ~~Info window~~		\| '''2'''
	\| ~~Shows~~ the ~~information for~~ the ~~current region.~~		\| Contig View
			\| The ''Contig View'' displays all visible regions of the selected contig. The visibility and colors can be adjusted in the preferences
	\|-		\|-
	\| ~~Action window~~		\| '''3'''
	\| ~~Shows~~ the ~~actions available for~~ the current region. This replaces the right mouse button ~~menu in~~ the GenDB GUI ~~interface~~.		\| Plot View
			\| The ''Plot View'' can display the GC-Plot, GC-Skew and the Frame-Plot. Each plot can be toggled with a click on its appropriate box in the legend
			\|-
			\| '''4'''
			\| QuickNav Bar
			\| The ''Quick Navigation Bar'' is used to easily jump to specific parts of the contig while displaying the current position with the red box. Simply click to move the red box
			\|-
			\| '''5'''
			\| Region Info
			\| This part shows all informations about the currently selected region. These are categorized in 3 categories: Region info, Annotation Region and Annotation Function
			\|-
			\| '''6'''
			\| Contig Info
			\| This part summarizes some statistics of the selected contig
			\|-
			\| '''7'''
			\| Action View
			\| This view replaces the right mouse button of the GenDB-GUI. All the actions from the ''right-click-menu'' moved to here
			\|-
			\| '''8'''
			\| Navigation
			\| With the arrows at the upper right/left corner you can navigate up-/downstream the contig

imported>AlexanderGoesmann at 08:58, 16 November 2004

2004-11-16T08:58:26Z

← Older revision		Revision as of 10:58, 16 November 2004
Line 2:		Line 2:
	= The GenDB web Contig View =		= The GenDB web Contig View =

	[[Image:GenDBWiki$$WebDocumentation$$MainViews$$ContigView$~~GenDBMain~~.png]]		[[Image:GenDBWiki$$WebDocumentation$$MainViews$$ContigView$GenDB22Main.png]]

	{\| border="1" cellpadding="2" cellspacing="0"		{\| border="1" cellpadding="2" cellspacing="0"

imported>AlexanderGoesmann at 08:54, 16 November 2004

2004-11-16T08:54:11Z

← Older revision		Revision as of 10:54, 16 November 2004
Line 1:		Line 1:
	__NOTOC__		__NOTOC__
	= The !GenDB web Contig View =		= The GenDB web Contig View =

	[[Image:GenDBWiki$$WebDocumentation$$MainViews$$ContigView$GenDBMain.png]]		[[Image:GenDBWiki$$WebDocumentation$$MainViews$$ContigView$GenDBMain.png]]

Unknown user at 00:00, 1 January 1970

1970-01-01T00:00:00Z

New page

__NOTOC__
= The !GenDB web Contig View =

[[Image:GenDBWiki$$WebDocumentation$$MainViews$$ContigView$GenDBMain.png]]

{| border="1" cellpadding="2" cellspacing="0"
| Menu Bar
| The menu bar on top of the window is the main navigation bar for the GenDB web interface.
|-
| Contig Selection
| Shows a list of contigs in the project. In addition the contig length, the number of regions in various states is listed.
|-
| Contig View
| Shows an overview of regions in the for the currently selected contig.
|-
| GC plot
| This window shows a GC and GC-skew plot for the part of sequence currently shown in the Contig View.
|-
| Quick navigation bar
| Clicking here moves the Contig View to the part of genome the user clicked. When multiple regions have been selected these are also shown here as ticks on the contig.
|-
| Info window
| Shows the information for the current region.
|-
| Action window
| Shows the actions available for the current region. This replaces the right mouse button menu in the GenDB GUI interface.