SEED Viewer Manual/GenomeBrowser - Revision history

DanielaBartels: /* The Control TabView */

2008-12-05T10:58:48Z

The Control TabView

TobiasPaczian: /* The Six Frame View */

2008-11-21T11:01:04Z

The Six Frame View

DanielaBartels: /* The Feature Table */

2008-11-21T10:59:17Z

The Feature Table

DanielaBartels: /* The Control TabView */

2008-11-21T10:55:23Z

The Control TabView

DanielaBartels: /* The Control TabView */

2008-11-21T10:30:08Z

The Control TabView

DanielaBartels: /* The Control TabView */

2008-11-21T10:22:37Z

The Control TabView

DanielaBartels: /* The Control TabView */

2008-11-21T10:18:45Z

The Control TabView

DanielaBartels: /* The Control TabView */

2008-11-21T10:12:27Z

The Control TabView

DanielaBartels: /* Genome Browser */

2008-11-21T10:09:08Z

Genome Browser

DanielaBartels: /* The Control TabView */

2008-11-21T10:07:15Z

The Control TabView

@@ Line 27: / Line 27: @@
 Clicking '''details page''' leads to the [[SEED_Viewer_Manual/Annotation|Annotation]] page of the feature. You will see all known details about the feature, as well as the [[SEED_Viewer_Manual/Annotation#CompareRegions|Compare regions view]] centered on the feature.
-The '''evidence''' button leads to the [[SEED_Viewer_Manual/Evidence|Evidence]] page showing evidence for the annotation of the feature in form of [[Glossary/Similarities|Similarities]] and protein domains.
+The '''evidence''' button leads to the [[SEED_Viewer_Manual/Evidence|Evidence]] page showing evidence for the annotation of the feature in form of Similarities and protein domains.
 '''Upload a list''' - will let you upload a list of locations of BLAST hits of the form (Contig, Start, Stop, ID). The list has to be in plain text format, meaning not an Excel table. If you have an Excel table containing the information, save the list as '''text (tab delimited)''' in Excel. If you have successfully uploaded a list, you will now be able to navigate the regions in your list. They are shown on the middle line in the Six Frame View in form of little boxes.

@@ Line 7: / Line 7: @@
 The six frame view represents the six reading frames for proteins (-3, -2, -1, 1, 2, 3). Blue arrows are printed representing protein features. Their direction depicts the strand of the protein (- or +).
-As RNA features (tRNAs, rRNAs, or other genomic features like binding sites) have no reading frames, they can be found in the middle line of the image, represented by little blue boxes.
+As RNA features (tRNAs, rRNAs, or other genomic features like binding sites) have no reading frames. They can be found in the middle line of the image, represented by little blue boxes.
 Hovering over a feature will show a tooltip containing information about the feature, including the name, the position in the genome, the [[Glossary#Functional_role|functional role]] and the [[Glossary#Subsystem|subsystem(s)]] it's in.

← Older revision		Revision as of 10:59, 21 November 2008
Line 34:		Line 34:

	=== The Feature Table ===		=== The Feature Table ===
		+
		+	The Feature Table shows all features present in your organism in a [[WebComponents/Table\|table]]. Information you can see for a feature are its ID, Type (e.g. CDS, RNA and others), its locations (Contig, Start, Stop) and length as well as the functional role it's annotated with and the subsystems it belongs to. The button in the last column (Region) will center the Six Frame View on this feature and select it.

	[[Image:GenomeBrowserFeat.png]]		[[Image:GenomeBrowserFeat.png]]

← Older revision		Revision as of 10:55, 21 November 2008
Line 28:		Line 28:

	The '''evidence''' button leads to the [[SEED_Viewer_Manual/Evidence\|Evidence]] page showing evidence for the annotation of the feature in form of [[Glossary/Similarities\|Similarities]] and protein domains.		The '''evidence''' button leads to the [[SEED_Viewer_Manual/Evidence\|Evidence]] page showing evidence for the annotation of the feature in form of [[Glossary/Similarities\|Similarities]] and protein domains.
		+
		+	'''Upload a list''' - will let you upload a list of locations of BLAST hits of the form (Contig, Start, Stop, ID). The list has to be in plain text format, meaning not an Excel table. If you have an Excel table containing the information, save the list as '''text (tab delimited)''' in Excel. If you have successfully uploaded a list, you will now be able to navigate the regions in your list. They are shown on the middle line in the Six Frame View in form of little boxes.

	[[Image:GenomeBrowserLoc.png]]		[[Image:GenomeBrowserLoc.png]]

@@ Line 23: / Line 23: @@
 If you have selected a feature in the Six Frame View, the second tab ('''Focus''') will show you information about the feature (the same information you can find in the tooltip by hovering over the feature). Additionally, you will get three buttons that lead to pages that show more detailed information about the selected feature.
-The button '''zoom to sequence''' will show you the '''[[SEED_Viewer_Manual/ContigView|DNA to Protein]] page depicting a detailed sequence view including the DNA sequence, a six frame view of the translation to protein and other features of the sequence in the area of the selected feature.
+The button '''zoom to sequence''' will show you the '''[[SEED_Viewer_Manual/ContigView|DNA to Protein]]''' page depicting a detailed sequence view including the DNA sequence, a six frame view of the translation to protein and other features of the sequence in the area of the selected feature.
 [[Image:GenomeBrowserLoc.png]]

@@ Line 21: / Line 21: @@
 Click the button '''Draw''' after making your selections. The arrows '''<=''' and '''=>''' will shift the  window over the contig sequence.
-If you have selected a feature in the Six Frame View, the second tab ('''Focus''') will show you information about the feature (the same information you can find in the tooltip by hovering over the feature). Additionally, you will get three buttons that lead to pages that show more detailed information of the selected sequence.
+If you have selected a feature in the Six Frame View, the second tab ('''Focus''') will show you information about the feature (the same information you can find in the tooltip by hovering over the feature). Additionally, you will get three buttons that lead to pages that show more detailed information about the selected feature.
 [[Image:GenomeBrowserLoc.png]]

← Older revision		Revision as of 10:18, 21 November 2008
Line 20:		Line 20:

	Click the button '''Draw''' after making your selections. The arrows '''<=''' and '''=>''' will shift the window over the contig sequence.		Click the button '''Draw''' after making your selections. The arrows '''<=''' and '''=>''' will shift the window over the contig sequence.
		+
		+	If you have selected a feature in the Six Frame View, the second tab ('''Focus''') will show you information about the feature (the same information you can find in the tooltip by hovering over the feature). Additionally, you will get three buttons that lead to pages that show more detailed information of the selected sequence.

	[[Image:GenomeBrowserLoc.png]]		[[Image:GenomeBrowserLoc.png]]

@@ Line 15: / Line 15: @@
 === The Control TabView ===
-Controlling the Six Frame View can be done using the first tab ('''Location''') of the Control TabView. You can choose a location the of the genome you want to view by selecting a contig in the '''contig''' drop down menu and stating a '''start position''' on that contig. The zoom of the window can be changed using the '''window''' drop down box. In addition, features can be colored by different metaphors: by subsystem, by filter options of the Feature Table (the features that are present in the table after filtering it will be colored) or by a user defined list you can specify in the '''Upload List''' tab. Click the button '''Draw''' after making your selections. The arrows '''<=''' and '''=>''' will shift the  window over the contig sequence.
+Controlling the Six Frame View can be done using the first tab ('''Location''') of the Control TabView. You can choose a location the of the genome you want to view by selecting a contig in the '''contig''' drop down menu and stating a '''start position''' on that contig. The zoom of the window can be changed using the '''window''' drop down box.
 [[Image:GenomeBrowserLoc.png]]
 [[Image:GenomeBrowserFeat.png]]