GenDBWiki/WebDocumentation/MainViews/ContigView: Difference between revisions

From BRF-Software
Jump to navigation Jump to search
imported>AlexanderGoesmann
No edit summary
imported>AlexanderLenhardt
No edit summary
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

Revision as of 15:31, 26 November 2004

The GenDB web Contig View

File:GenDBWiki$$WebDocumentation$$MainViews$$ContigView$GenDB22bMain.png

1 Menu Bar The menu bar on top of the window is the main navigation bar for the GenDB web interface.
Contig shows you a list of available contigs in this project. This list is ordered by ascending length of the contigs.
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
With Classification you can choose between three common classification systems namely GO, KEGG and COG
Preferences has a submenu to call the preferences dialog and an option to view/hide the region observations in the Contig View
2 Contig View The Contig View displays all visible regions of the selected contig. The visibility and colors can be adjusted in the preferences
3 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
Retrieved from "https://wiki.cebitec.uni-bielefeld.de/brf-software/index.php?title=GenDBWiki/WebDocumentation/MainViews/ContigView&oldid=2161"