GenDBWiki/WebDocumentation/DialogWindows/ClusterTool - Revision history

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2011-10-26T06:16:14Z

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← Older revision	Revision as of 08:16, 26 October 2011
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imported>NilsKleinboelting at 13:30, 21 March 2006

2006-03-21T13:30:48Z

← Older revision		Revision as of 15:30, 21 March 2006
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	# depending on the number of clusters found, the tool may need some time until the results are computed		# depending on the number of clusters found, the tool may need some time until the results are computed
	<br>		<br>
			== Summary ==
	This is the first part of the Cluster-Tool-Result. You get some statistics how many clusters were found and how big they are. Then you get two tables where subsystems and roles are listed for the CDS that are similar to your input-CDS. For more information about subsystems and roles see: [http://theseed.uchicago.edu/FIG/index.cgi SEED].<br>		This is the first part of the Cluster-Tool-Result. You get some statistics how many clusters were found and how big they are. Then you get two tables where subsystems and roles are listed for the CDS that are similar to your input-CDS. For more information about subsystems and roles see: [http://theseed.uchicago.edu/FIG/index.cgi SEED].<br>
	<br>		<br>
	[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$ClusterTool$ClusterTool_summary.gif]]		[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$ClusterTool$ClusterTool_summary.gif]]
	<br><br>		<br><br>
			== Cluster - Visualisation ==
			The second part of the result is a visualisation of the clusters. You can see the examined CDS from GenDB and its neighbourhood. You can get more information about each CDS by tooltips. Below you can see the CDS that corresponds to the Blast-hit you used, its neighbourhood and similar clusters in other genomes. Similar colours mean that the CDS are similar (Blast-hits). By clicking a CDS here you are linked to the corresponding entry in the SEED-Database.
			<br><br>
			[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$ClusterTool$ClusterTool_clusters.gif]]

			=== Changing the examined neighbourhood ===
	By default the examined neighbourhood is 5000 bases - so all CDS 5000 bases upstream and downstream with regard to the input-CDS are found, if they are conserved in other genomes. You can change this value and recompute the results. Other neighbourhoods then 5000 are not precomputed, so the computation may take a while.		By default the examined neighbourhood is 5000 bases - so all CDS 5000 bases upstream and downstream with regard to the input-CDS are found, if they are conserved in other genomes. You can change this value and recompute the results. Other neighbourhoods then 5000 are not precomputed, so the computation may take a while.
	<br><br>		<br><br>
	[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$ClusterTool$ClusterTool_neighbourhood.gif]]		[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$ClusterTool$ClusterTool_neighbourhood.gif]]
	~~<br>~~

	The second part of the result is a visualisation of the clusters. You can see the examined CDS from GenDB and its neighbourhood. You can get more information about each CDS by tooltips. Below you can see the CDS that corresponds to the Blast-hit you used, its neighbourhood and similar clusters in other genomes. Similar colours mean that the CDS are similar (Blast-hits). By clicking a CDS here you are linked to the corresponding entry in the SEED-Database.
	~~<br><br>~~
	~~[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$ClusterTool$ClusterTool_clusters.gif]]~~

	For more information about the Cluster-Tool see [[Media:GenDBWiki$$WebDocumentation$$DialogWindows$$ClusterTool$ClusterTool_Bachelorarbeit.pdf\|here]].		For more information about the Cluster-Tool see [[Media:GenDBWiki$$WebDocumentation$$DialogWindows$$ClusterTool$ClusterTool_Bachelorarbeit.pdf\|here]].

imported>NilsKleinboelting at 13:29, 21 March 2006

2006-03-21T13:29:01Z

← Older revision		Revision as of 15:29, 21 March 2006
Line 19:		Line 19:

	The second part of the result is a visualisation of the clusters. You can see the examined CDS from GenDB and its neighbourhood. You can get more information about each CDS by tooltips. Below you can see the CDS that corresponds to the Blast-hit you used, its neighbourhood and similar clusters in other genomes. Similar colours mean that the CDS are similar (Blast-hits). By clicking a CDS here you are linked to the corresponding entry in the SEED-Database.		The second part of the result is a visualisation of the clusters. You can see the examined CDS from GenDB and its neighbourhood. You can get more information about each CDS by tooltips. Below you can see the CDS that corresponds to the Blast-hit you used, its neighbourhood and similar clusters in other genomes. Similar colours mean that the CDS are similar (Blast-hits). By clicking a CDS here you are linked to the corresponding entry in the SEED-Database.
	<br>		<br><br>
	[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$ClusterTool$ClusterTool_clusters.gif]]		[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$ClusterTool$ClusterTool_clusters.gif]]

	For more information about the Cluster-Tool see [[Media:GenDBWiki$$WebDocumentation$$DialogWindows$$ClusterTool$ClusterTool_Bachelorarbeit.pdf\|here]].		For more information about the Cluster-Tool see [[Media:GenDBWiki$$WebDocumentation$$DialogWindows$$ClusterTool$ClusterTool_Bachelorarbeit.pdf\|here]].

imported>NilsKleinboelting at 13:28, 21 March 2006

2006-03-21T13:28:42Z

← Older revision		Revision as of 15:28, 21 March 2006
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	# have a look at the observations - there is a link in the DB-column, where you can start the Cluster-Tool		# have a look at the observations - there is a link in the DB-column, where you can start the Cluster-Tool
	# depending on the number of clusters found, the tool may need some time until the results are computed		# depending on the number of clusters found, the tool may need some time until the results are computed
	~~<br>~~<br>		<br>
	This is the first part of the Cluster-Tool-Result. You get some statistics how many clusters were found and how big they are. Then you get two tables where subsystems and roles are listed for the CDS that are similar to your input-CDS. For more information about subsystems and roles see: [http://theseed.uchicago.edu/FIG/index.cgi SEED].<br>		This is the first part of the Cluster-Tool-Result. You get some statistics how many clusters were found and how big they are. Then you get two tables where subsystems and roles are listed for the CDS that are similar to your input-CDS. For more information about subsystems and roles see: [http://theseed.uchicago.edu/FIG/index.cgi SEED].<br>
	<br>		<br>
Line 19:		Line 19:

	The second part of the result is a visualisation of the clusters. You can see the examined CDS from GenDB and its neighbourhood. You can get more information about each CDS by tooltips. Below you can see the CDS that corresponds to the Blast-hit you used, its neighbourhood and similar clusters in other genomes. Similar colours mean that the CDS are similar (Blast-hits). By clicking a CDS here you are linked to the corresponding entry in the SEED-Database.		The second part of the result is a visualisation of the clusters. You can see the examined CDS from GenDB and its neighbourhood. You can get more information about each CDS by tooltips. Below you can see the CDS that corresponds to the Blast-hit you used, its neighbourhood and similar clusters in other genomes. Similar colours mean that the CDS are similar (Blast-hits). By clicking a CDS here you are linked to the corresponding entry in the SEED-Database.

	<br>		<br>
	[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$ClusterTool$ClusterTool_clusters.gif]]		[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$ClusterTool$ClusterTool_clusters.gif]]

	For more information about the Cluster-Tool see [[Media:GenDBWiki$$WebDocumentation$$DialogWindows$$ClusterTool$ClusterTool_Bachelorarbeit.pdf\|here]].		For more information about the Cluster-Tool see [[Media:GenDBWiki$$WebDocumentation$$DialogWindows$$ClusterTool$ClusterTool_Bachelorarbeit.pdf\|here]].

imported>NilsKleinboelting at 13:27, 21 March 2006

2006-03-21T13:27:57Z

← Older revision		Revision as of 15:27, 21 March 2006
Line 12:		Line 12:
	<br>		<br>
	[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$ClusterTool$ClusterTool_summary.gif]]		[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$ClusterTool$ClusterTool_summary.gif]]
	<br>		<br><br>
	By default the examined neighbourhood is 5000 bases - so all CDS 5000 bases upstream and downstream with regard to the input-CDS are found, if they are conserved in other genomes. You can change this value and recompute the results. Other neighbourhoods then 5000 are not precomputed, so the computation may take a while.		By default the examined neighbourhood is 5000 bases - so all CDS 5000 bases upstream and downstream with regard to the input-CDS are found, if they are conserved in other genomes. You can change this value and recompute the results. Other neighbourhoods then 5000 are not precomputed, so the computation may take a while.
	<br>		<br><br>
	[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$ClusterTool$ClusterTool_neighbourhood.gif]]		[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$ClusterTool$ClusterTool_neighbourhood.gif]]
	<br>		<br>

imported>NilsKleinboelting at 13:27, 21 March 2006

2006-03-21T13:27:29Z

← Older revision		Revision as of 15:27, 21 March 2006
Line 12:		Line 12:
	<br>		<br>
	[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$ClusterTool$ClusterTool_summary.gif]]		[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$ClusterTool$ClusterTool_summary.gif]]
			<br>
			By default the examined neighbourhood is 5000 bases - so all CDS 5000 bases upstream and downstream with regard to the input-CDS are found, if they are conserved in other genomes. You can change this value and recompute the results. Other neighbourhoods then 5000 are not precomputed, so the computation may take a while.
			<br>
			[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$ClusterTool$ClusterTool_neighbourhood.gif]]
	<br>		<br>

imported>NilsKleinboelting at 16:12, 6 March 2006

2006-03-06T16:12:24Z

← Older revision		Revision as of 18:12, 6 March 2006
Line 14:		Line 14:
	<br>		<br>

	The second part of the result is a visualisation of the clusters. You can see the examined CDS from GenDB and its neighbourhood. You can get more information about each CDS by tooltips. Below you can see the CDS that corresponds to the Blast-hit you used, its neighbourhood and similar clusters in other genomes. Similar colours mean that the CDS are similar (Blast-hits).		The second part of the result is a visualisation of the clusters. You can see the examined CDS from GenDB and its neighbourhood. You can get more information about each CDS by tooltips. Below you can see the CDS that corresponds to the Blast-hit you used, its neighbourhood and similar clusters in other genomes. Similar colours mean that the CDS are similar (Blast-hits). By clicking a CDS here you are linked to the corresponding entry in the SEED-Database.

	<br>		<br>
	[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$ClusterTool$ClusterTool_clusters.gif]]		[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$ClusterTool$ClusterTool_clusters.gif]]

	[[Media:GenDBWiki$$WebDocumentation$$DialogWindows$$ClusterTool$ClusterTool_Bachelorarbeit.pdf]]		For more information about the Cluster-Tool see [[Media:GenDBWiki$$WebDocumentation$$DialogWindows$$ClusterTool$ClusterTool_Bachelorarbeit.pdf\|here]].

imported>NilsKleinboelting at 16:10, 6 March 2006

2006-03-06T16:10:35Z

← Older revision		Revision as of 18:10, 6 March 2006
Line 12:		Line 12:
	<br>		<br>
	[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$ClusterTool$ClusterTool_summary.gif]]		[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$ClusterTool$ClusterTool_summary.gif]]
			<br>

			The second part of the result is a visualisation of the clusters. You can see the examined CDS from GenDB and its neighbourhood. You can get more information about each CDS by tooltips. Below you can see the CDS that corresponds to the Blast-hit you used, its neighbourhood and similar clusters in other genomes. Similar colours mean that the CDS are similar (Blast-hits).

			<br>
	[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$ClusterTool$ClusterTool_clusters.gif]]		[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$ClusterTool$ClusterTool_clusters.gif]]

	[[Media:GenDBWiki$$WebDocumentation$$DialogWindows$$ClusterTool$ClusterTool_Bachelorarbeit.pdf]]		[[Media:GenDBWiki$$WebDocumentation$$DialogWindows$$ClusterTool$ClusterTool_Bachelorarbeit.pdf]]

imported>NilsKleinboelting at 15:43, 6 March 2006

2006-03-06T15:43:54Z

← Older revision		Revision as of 17:43, 6 March 2006
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	__NOTOC__		__NOTOC__
	=Cluster-Tool=		= Cluster-Tool =

	The Cluster-Tool can be used to search for conserved gene-clusters. To use the tool you must do the following:		The Cluster-Tool can be used to search for conserved gene-clusters. To use the tool you must do the following:

imported>NilsKleinboelting at 15:43, 6 March 2006

2006-03-06T15:43:17Z

← Older revision		Revision as of 17:43, 6 March 2006
Line 9:		Line 9:
	# depending on the number of clusters found, the tool may need some time until the results are computed		# depending on the number of clusters found, the tool may need some time until the results are computed
	<br><br>		<br><br>
	This is the first part of the Cluster-Tool-Result. You get some statistics how many clusters were found and how big they are. Then you get two tables where subsystems and roles are listed for the CDS that are similar to your input-CDS. For more information about subsystems and roles see: [http://theseed.uchicago.edu/FIG/index.cgi SEED]		This is the first part of the Cluster-Tool-Result. You get some statistics how many clusters were found and how big they are. Then you get two tables where subsystems and roles are listed for the CDS that are similar to your input-CDS. For more information about subsystems and roles see: [http://theseed.uchicago.edu/FIG/index.cgi SEED].<br>
			<br>
	[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$ClusterTool$ClusterTool_summary.gif]]		[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$ClusterTool$ClusterTool_summary.gif]]
	[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$ClusterTool$ClusterTool_clusters.gif]]		[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$ClusterTool$ClusterTool_clusters.gif]]

	[[Media:GenDBWiki$$WebDocumentation$$DialogWindows$$ClusterTool$ClusterTool_Bachelorarbeit.pdf]]		[[Media:GenDBWiki$$WebDocumentation$$DialogWindows$$ClusterTool$ClusterTool_Bachelorarbeit.pdf]]