GenDBWiki/WebDocumentation/DialogWindows/ComparativeAnnotator - Revision history

Agoesman at 20:06, 15 November 2011

2011-11-15T20:06:08Z

Admin: 27 revisions

2011-10-26T06:18:20Z

27 revisions

← Older revision	Revision as of 08:18, 26 October 2011
(No difference)

imported>AlexanderGoesmann at 12:51, 6 March 2006

2006-03-06T12:51:40Z

imported>NilsKleinboelting at 17:13, 3 March 2006

2006-03-03T17:13:43Z

← Older revision		Revision as of 19:13, 3 March 2006
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	The second part of the window shows Blast-Hits between the detected CDS. Green Arrows mean a Blast-Hit with an eValue smaller then 1.0e-10, red arrows mean blast hits with an evalue greater then 1.0e-10.<br>		The second part of the window shows Blast-Hits between the detected CDS. Green Arrows mean a Blast-Hit with an eValue smaller then 1.0e-10, red arrows mean blast hits with an evalue greater then 1.0e-10.<br>
	On the righten side of the image you get some information about the selected CDS. By clicking on a CDS you can select others.		On the righten side of the image you get some information about the selected CDS. By clicking on a CDS you can select others.
	<br>		<br><br>
	[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$ComparativeAnnotator$compAnno_part2.gif]]		[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$ComparativeAnnotator$compAnno_part2.gif]]

	==== View aligment ====		==== View aligment ====
	You can have a look at an alignment by clicking on an arrow and selecting '''"Result"'''<br>		You can have a look at an alignment by clicking on an arrow and selecting '''"Result"'''<br><br>
	[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$ComparativeAnnotator$compAnno_alignment.gif]]		[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$ComparativeAnnotator$compAnno_alignment.gif]]

imported>NilsKleinboelting at 17:13, 3 March 2006

2006-03-03T17:13:13Z

← Older revision		Revision as of 19:13, 3 March 2006
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	==== Other similar CDS ====		==== Other similar CDS ====
	Under '''"Other similar CDS"''' in the detail-view of an CDS you can see some other good Blast Hits. By clicking them you can call the Comparative Annotator for that CDS.<br>		Under '''"Other similar CDS"''' in the detail-view of an CDS you can see some other good Blast Hits. By clicking them you can call the Comparative Annotator for that CDS.<br><br>
	[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$ComparativeAnnotator$compAnno_otherSimilar.gif]]		[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$ComparativeAnnotator$compAnno_otherSimilar.gif]]

imported>NilsKleinboelting at 17:09, 3 March 2006

2006-03-03T17:09:35Z

← Older revision		Revision as of 19:09, 3 March 2006
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	== CDS Comparison ==		== CDS Comparison ==
			<br>
			The second part of the window shows Blast-Hits between the detected CDS. Green Arrows mean a Blast-Hit with an eValue smaller then 1.0e-10, red arrows mean blast hits with an evalue greater then 1.0e-10.<br>
			On the righten side of the image you get some information about the selected CDS. By clicking on a CDS you can select others.
			<br>
	[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$ComparativeAnnotator$compAnno_part2.gif]]		[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$ComparativeAnnotator$compAnno_part2.gif]]

	==== View aligment ====		==== View aligment ====
			You can have a look at an alignment by clicking on an arrow and selecting '''"Result"'''<br>
	[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$ComparativeAnnotator$compAnno_alignment.gif]]		[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$ComparativeAnnotator$compAnno_alignment.gif]]

	==== Other similar CDS ====		==== Other similar CDS ====
			Under '''"Other similar CDS"''' in the detail-view of an CDS you can see some other good Blast Hits. By clicking them you can call the Comparative Annotator for that CDS.<br>
	[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$ComparativeAnnotator$compAnno_otherSimilar.gif]]		[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$ComparativeAnnotator$compAnno_otherSimilar.gif]]

imported>NilsKleinboelting at 16:59, 3 March 2006

2006-03-03T16:59:02Z

← Older revision		Revision as of 18:59, 3 March 2006
Line 26:		Line 26:
	You can select one CDS as reference and annotate it (or check if it is correct), using the [[GenDBWiki/WebDocumentation/DialogWindows/AnnotationDialog\|Annotation Dialog]].<br>		You can select one CDS as reference and annotate it (or check if it is correct), using the [[GenDBWiki/WebDocumentation/DialogWindows/AnnotationDialog\|Annotation Dialog]].<br>
	- select the desired CDS as '''Reference'''<br>		- select the desired CDS as '''Reference'''<br>
	- click the '''"Annotate Reference"''' - ~~Button~~<br>		- click the '''"Annotate Reference"''' - button<br>
	- do your annotation<br>		- do your annotation<br>

Line 37:		Line 37:
	- select the CDS whose annotation you want to copy as '''Reference'''<br>		- select the CDS whose annotation you want to copy as '''Reference'''<br>
	- select the CDSs where you want the annotation to be copied as '''Annotate'''<br>		- select the CDSs where you want the annotation to be copied as '''Annotate'''<br>
	- click the '''"Copy Annotation"''' - ~~Button~~ <br>		- click the '''"Copy Annotation"''' - button <br>
	[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$ComparativeAnnotator$compAnno_copyAnnot1.gif]]		[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$ComparativeAnnotator$compAnno_copyAnnot1.gif]]

	- when you are sure that you want to copy the annotation, click '~~yes~~'<br>		- when you are sure that you want to copy the annotation, click '''"OK"'''<br>

	[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$ComparativeAnnotator$compAnno_copyAnnot2.gif]]		[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$ComparativeAnnotator$compAnno_copyAnnot2.gif]]
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	<span id="ViewMultipleAlignment"></span>		<span id="ViewMultipleAlignment"></span>
	==== View multiple alignment ====		==== View multiple alignment ====

			You can compute a multiple Alignment of two or more CDS with ClustalW.<br>
			- choose two ore more CDS with the '''"mult. Alignment"'''-Checkboxes<br>
			- click the '''"View multiple alignment"'''-button <br>
			- wait for the result<br>

	[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$ComparativeAnnotator$compAnno_multAlign.gif]]		[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$ComparativeAnnotator$compAnno_multAlign.gif]]
			<br>

	== CDS Comparison ==		== CDS Comparison ==

imported>NilsKleinboelting at 16:55, 3 March 2006

2006-03-03T16:55:45Z

← Older revision		Revision as of 18:55, 3 March 2006
Line 25:		Line 25:

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

Line 35:		Line 35:

	You can copy the annotation from one CDS to others.<br>		You can copy the annotation from one CDS to others.<br>
	- select the CDS whose annotation you want to copy as '''~~reference~~'''<br>		- select the CDS whose annotation you want to copy as '''Reference'''<br>
	- select the CDSs where you want the annotation to be copied as '''Annotate'''<br>		- select the CDSs where you want the annotation to be copied as '''Annotate'''<br>
	- click the "Copy Annotation" - Button <br>		- click the '''"Copy Annotation"''' - Button <br>
	[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$ComparativeAnnotator$compAnno_copyAnnot1.gif]]		[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$ComparativeAnnotator$compAnno_copyAnnot1.gif]]

imported>NilsKleinboelting at 16:54, 3 March 2006

2006-03-03T16:54:58Z

← Older revision		Revision as of 18:54, 3 March 2006
Line 43:		Line 43:

	[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$ComparativeAnnotator$compAnno_copyAnnot2.gif]]		[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$ComparativeAnnotator$compAnno_copyAnnot2.gif]]

			- The annotations are now copied <br>
			<br>

	<span id="ViewMultipleAlignment"></span>		<span id="ViewMultipleAlignment"></span>

imported>NilsKleinboelting at 16:53, 3 March 2006

2006-03-03T16:53:10Z

← Older revision		Revision as of 18:53, 3 March 2006
Line 34:		Line 34:
	==== Copy Annotation ====		==== Copy Annotation ====

			You can copy the annotation from one CDS to others.<br>
			- select the CDS whose annotation you want to copy as '''reference'''<br>
			- select the CDSs where you want the annotation to be copied as '''Annotate'''<br>
			- click the "Copy Annotation" - Button <br>
	[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$ComparativeAnnotator$compAnno_copyAnnot1.gif]]		[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$ComparativeAnnotator$compAnno_copyAnnot1.gif]]

			- when you are sure that you want to copy the annotation, click 'yes'<br>

	[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$ComparativeAnnotator$compAnno_copyAnnot2.gif]]		[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$ComparativeAnnotator$compAnno_copyAnnot2.gif]]

← Older revision		Revision as of 22:06, 15 November 2011
Line 18:		Line 18:
	On the right side of the image you can do the following:		On the right side of the image you can do the following:
	* [[#AnnotateReference\|Annotate the Reference]]		* [[#AnnotateReference\|Annotate the Reference]]
	* [[#CopyAnnotation\|Copy Annotation]]		* [[#CopyAnnotation\|Copy Annotation]]
	* [[#ViewMultipleAlignment\|View multiple alignment]]		* [[#ViewMultipleAlignment\|View multiple alignment]]

Line 25:		Line 25:

	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>		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>		- select the desired CDS as '''Reference'''<br>
	- click the '''"Annotate Reference"''' - button<br>		- click the '''"Annotate Reference"''' - button<br>
	- do your annotation<br>		- do your annotation<br>

	[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$ComparativeAnnotator$compAnno_annotateReference.gif]]		[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$ComparativeAnnotator$compAnno_annotateReference.gif]]
Line 35:		Line 35:

	You can copy the annotation from one CDS to others.<br>		You can copy the annotation from one CDS to others.<br>
	- select the CDS with the annotation you want to copy as '''Reference'''<br>		- select the CDS with the annotation you want to copy as '''Reference'''<br>
	- select the CDSs where you want the annotation to be copied as '''Annotate'''<br>		- select the CDSs where you want the annotation to be copied as '''Annotate'''<br>
	- click the '''"Copy Annotation"''' - button <br>		- click the '''"Copy Annotation"''' - button <br>
	[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$ComparativeAnnotator$compAnno_copyAnnot1.gif]]		[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$ComparativeAnnotator$compAnno_copyAnnot1.gif]]

	- when you are sure that you want to copy the annotation, click '''"OK"'''<br>		- when you are sure that you want to copy the annotation, click '''"OK"'''<br>

	[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$ComparativeAnnotator$compAnno_copyAnnot2.gif]]		[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$ComparativeAnnotator$compAnno_copyAnnot2.gif]]

	- The annotations are now copied <br>		- The annotations are now copied <br>
	<br>		<br>

Line 51:		Line 51:

	You can compute a multiple Alignment of two or more CDS with ClustalW.<br>		You can compute a multiple Alignment of two or more CDS with ClustalW.<br>
	- choose two ore more CDS with the '''"mult. Alignment"'''-Checkboxes<br>		- choose two ore more CDS with the '''"mult. Alignment"'''-Checkboxes<br>
	- click the '''"View multiple alignment"'''-button <br>		- click the '''"View multiple alignment"'''-button <br>
	- wait for the result<br>		- wait for the result<br>

	[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$ComparativeAnnotator$compAnno_multAlign.gif]]		[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$ComparativeAnnotator$compAnno_multAlign.gif]]

← Older revision		Revision as of 14:51, 6 March 2006
Line 2:		Line 2:
	= Comparative Annotator =		= Comparative Annotator =

	The Comparative Annotator is a tool that can be used to find similar CDS in related organisms and to annotate them ~~consistent through their~~ genomes.<br>		The Comparative Annotator is a tool that can be used to find similar CDS in related organisms and to annotate them consistently in all genomes.<br>
	<br>		<br>
	What should be done to use this tool?<br>		What should be done to use this tool?<br>
Line 12:		Line 12:
	== Genome View ==		== Genome View ==

	In the first part of the window, you can see the detected CDS and their neighbourhoods. You can navigate through the genomes by clicking the CDS - the CDS will be centered and you get the Comparative Annotator for that CDS. You can get ~~informations~~ about the CDS by tooltips.		In the first part of the window, you can see the detected CDS and their neighbourhoods. You can navigate through the genomes by clicking the CDS - the CDS will be centered and you get the Comparative Annotator for that CDS. You can get information about the CDS by tooltips.

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

	On the ~~righten~~ side of the image you can do the following:		On the right side of the image you can do the following:
	* [[#AnnotateReference\|Annotate the Reference]]		* [[#AnnotateReference\|Annotate the Reference]]
	* [[#CopyAnnotation\|Copy Annotation]]		* [[#CopyAnnotation\|Copy Annotation]]
Line 24:		Line 24:
	==== Annotate the reference ====		==== Annotate the reference ====

	You can select one CDS as reference and annotate it (or check if it is correct), using the [[GenDBWiki/WebDocumentation/DialogWindows/AnnotationDialog\|Annotation Dialog]].<br>		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>		- select the desired CDS as '''Reference'''<br>
	- click the '''"Annotate Reference"''' - button<br>		- click the '''"Annotate Reference"''' - button<br>
Line 35:		Line 35:

	You can copy the annotation from one CDS to others.<br>		You can copy the annotation from one CDS to others.<br>
	- select the CDS ~~whose~~ annotation you want to copy as '''Reference'''<br>		- select the CDS with the annotation you want to copy as '''Reference'''<br>
	- select the CDSs where you want the annotation to be copied as '''Annotate'''<br>		- select the CDSs where you want the annotation to be copied as '''Annotate'''<br>
	- click the '''"Copy Annotation"''' - button <br>		- click the '''"Copy Annotation"''' - button <br>
Line 60:		Line 60:
	== CDS Comparison ==		== CDS Comparison ==
	<br>		<br>
	The second part of the window shows Blast-Hits between the detected CDS. Green ~~Arrows mean~~ a Blast~~-Hit~~ with an ~~eValue~~ smaller then 1.0e-10, red arrows ~~mean blast~~ hits with an ~~evalue~~ greater then 1.0e-10.<br>		The second part of the window shows Blast-Hits between the detected CDS. Green arrows indicate a Blast hit with an e-value smaller then 1.0e-10, red arrows indicate Blast hits with an e-value greater then 1.0e-10.<br>
	On the ~~righten~~ side of the image you get some information about the selected CDS. By clicking on a CDS you can select others.		On the right side of the image you get some information about the selected CDS. By clicking on a CDS you can select others.
	<br><br>		<br><br>
	[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$ComparativeAnnotator$compAnno_part2.gif]]		[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$ComparativeAnnotator$compAnno_part2.gif]]
Line 70:		Line 70:

	==== Other similar CDS ====		==== Other similar CDS ====
	Under '''"Other similar CDS"''' in the detail-view of an CDS you can see some other good Blast Hits. By clicking them you can call the Comparative Annotator for that CDS.<br><br>		Under '''"Other similar CDS"''' in the detail-view of a CDS you can see some other good Blast Hits. By clicking them you can call the Comparative Annotator for that CDS.<br><br>
	[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$ComparativeAnnotator$compAnno_otherSimilar.gif]]		[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$ComparativeAnnotator$compAnno_otherSimilar.gif]]