GenDBWiki/WebDocumentation/DialogWindows/OrthologViewer - Revision history

Admin: 7 revisions

2011-10-26T06:14:57Z

7 revisions

← Older revision	Revision as of 08:14, 26 October 2011
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imported>NilsKleinboelting at 11:03, 6 December 2006

2006-12-06T11:03:28Z

← Older revision		Revision as of 13:03, 6 December 2006
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	[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$OrthologViewer$ortholog_viewer_3.gif]]		[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$OrthologViewer$ortholog_viewer_3.gif]]

			After selecting a CDS you get a menu:

			[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$OrthologViewer$ortholog_viewer_4.gif]]

			You can open the [[GenDBWiki/WebDocumentation/DialogWindows/ComparativeAnnotator\|Comparative Annotator]] or select the chosen CDS in the Main-Window.

imported>NilsKleinboelting at 10:49, 6 December 2006

2006-12-06T10:49:50Z

← Older revision		Revision as of 12:49, 6 December 2006
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	<span id="SelectCDS"></span>		<span id="SelectCDS"></span>
	==== Select a CDS ====		==== Select a CDS ====
	By clicking a CDS-box, one CDS is selected (red) and its orthologs are shown ~~orange~~.		By clicking a CDS-box, one CDS is selected (red) and its orthologs are marked orange. Information about all highlighted CDS are shown below the image. Loading the information may take some seconds. Please be patient. <br>

	[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$OrthologViewer$ortholog_viewer_3.gif]]		[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$OrthologViewer$ortholog_viewer_3.gif]]

imported>NilsKleinboelting at 11:18, 5 December 2006

2006-12-05T11:18:35Z

← Older revision		Revision as of 13:18, 5 December 2006
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	You can browse through the genome, using the scrollbar. When moving the mouse over a CDS-box, its orthologs are highlighted yellow:<br>		You can browse through the genome, using the scrollbar. When moving the mouse over a CDS-box, its orthologs are highlighted yellow:<br>
	[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$OrthologViewer$ortholog_viewer_2.gif]]		[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$OrthologViewer$ortholog_viewer_2.gif]]

	When you find an interesting CDS you may examine it further by selecting it.<br>		When you find an interesting CDS you may examine it further by selecting it.<br>

imported>NilsKleinboelting at 11:17, 5 December 2006

2006-12-05T11:17:52Z

← Older revision		Revision as of 13:17, 5 December 2006
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	[[Anchor(Browse Orthologs)]]		[[Anchor(Browse Orthologs)]]
	==== Browse through the genome ====		==== Browse through the genome ====
			You can browse through the genome, using the scrollbar. When moving the mouse over a CDS-box, its orthologs are highlighted yellow:<br>
			[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$OrthologViewer$ortholog_viewer_2.gif]]
			When you find an interesting CDS you may examine it further by selecting it.<br>

	<span id="SelectCDS"></span>		<span id="SelectCDS"></span>
	==== Select a CDS ====		==== Select a CDS ====
			By clicking a CDS-box, one CDS is selected (red) and its orthologs are shown orange.

			[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$OrthologViewer$ortholog_viewer_3.gif]]

imported>NilsKleinboelting at 10:56, 5 December 2006

2006-12-05T10:56:28Z

← Older revision		Revision as of 12:56, 5 December 2006
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	The Ortholog Viewer is a tool that shows ortholog CDS in similar genomes. The orthologs have to be computed before.<br>		The Ortholog Viewer is a tool that shows ortholog CDS in similar genomes. The orthologs have to be computed before.<br>
	<br>		<br>
	What should be done to use this tool?<br>		What should be done to use this tool? (Points 1-3 are already done, if you prepared the project for the [[GenDBWiki/WebDocumentation/DialogWindows/ComparativeAnnotator\|Comparative Annotator]]<br>
	# create Bidirectional-Blast-Tools in the project with: ''create_genome_compare_tools.pl''<br>		# create Bidirectional-Blast-Tools in the project with: ''create_genome_compare_tools.pl''<br>
	# Run the Tool for each Contig-combination with: ''submit_job.pl''<br>		# Run the Tool for each Contig-combination with: ''submit_job.pl''<br>
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	# Use the tool<br>		# Use the tool<br>
	<br>		<br>
	~~== Contig View ==~~
			This is how the window looks like after opening the Ortholog Viewer:<br>

	[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$OrthologViewer$ortholog_viewer_1.gif]]		[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$OrthologViewer$ortholog_viewer_1.gif]]

	~~On the right side of the image~~ you can do the following:		Now you can do the following:
	* [[#~~AnnotateReference~~\|~~Annotate~~ the ~~Reference]]~~		* [[#BrowseOrthologs\|Browse through the genome]]
	* [[#CopyAnnotation\|Copy Annotation]]		* [[#SelectCDS\|Select a CDS]]
	* [[#~~ViewMultipleAlignment\|View multiple alignment]]~~

	~~<span id="AnnotateReference"></span>~~
	~~==== Annotate the reference ====~~

	~~You can select one CDS as reference and annotate it (or check if the annotation is correct), using the [[GenDBWiki/WebDocumentation/DialogWindows/AnnotationDialog~~\|~~Annotation Dialog]].<br>~~
	~~- select the desired~~ CDS ~~as '''Reference'''<br>~~
	~~- click the '''"Annotate Reference"''' - button<br>~~
	~~- do your annotation<br>~~

	~~[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$OrthologViewer$compAnno_annotateReference.gif~~]]

	~~<span id="CopyAnnotation"></span>~~		[[Anchor(Browse Orthologs)]]
	==== ~~Copy Annotation~~ ====		==== Browse through the genome ====

	~~You can copy the annotation from one CDS to others.~~<br>		<span id="SelectCDS"></span>
			==== Select a CDS ====

imported>NilsKleinboelting at 10:48, 5 December 2006

2006-12-05T10:48:20Z

← Older revision		Revision as of 12:48, 5 December 2006
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	== Contig View ==		== Contig View ==

	[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$OrthologViewer$~~compAnno_part1~~.gif]]		[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$OrthologViewer$ortholog_viewer_1.gif]]

	On the right side of the image you can do the following:		On the right side of the image you can do the following:

imported>NilsKleinboelting at 10:47, 5 December 2006

2006-12-05T10:47:21Z

New page

__NOTOC__
= Ortholog Viewer =

The Ortholog Viewer is a tool that shows ortholog CDS in similar genomes. The orthologs have to be computed before. 
 
What should be done to use this tool? 
# create Bidirectional-Blast-Tools in the project with: ''create_genome_compare_tools.pl'' 
# Run the Tool for each Contig-combination with: ''submit_job.pl'' 
# Run ''set_biderectional_project_config.pl''. 
# Run ''compute_orthologs.pl'' to create ortholog-observations 
# Use the tool 
 
== Contig View ==

[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$OrthologViewer$compAnno_part1.gif]]

On the right side of the image you can do the following:
* [[#AnnotateReference|Annotate the Reference]]
* [[#CopyAnnotation|Copy Annotation]]
* [[#ViewMultipleAlignment|View multiple alignment]]


==== Annotate the reference ====

You can select one CDS as reference and annotate it (or check if the annotation is correct), using the [[GenDBWiki/WebDocumentation/DialogWindows/AnnotationDialog|Annotation Dialog]]. 
- select the desired CDS as '''Reference''' 
- click the '''"Annotate Reference"''' - button 
- do your annotation 

[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$OrthologViewer$compAnno_annotateReference.gif]]


==== Copy Annotation ====

You can copy the annotation from one CDS to others.