GenDBWiki/WebDocumentation/MainViews/ContigView: Difference between revisions
Jump to navigation
Jump to search
m (5 revisions) |
No edit summary |
||
| Line 2: | Line 2: | ||
= The GenDB web Contig View = | = The GenDB web Contig View = | ||
[[ | [[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 | ||
Latest revision as of 16:17, 10 November 2011
The GenDB web Contig View
| 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 |