GenDBWiki/WebDocumentation/DialogWindows/ClusterTool: Difference between revisions
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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: | ||
<br> | <br> | ||
# create a Blast vs. Seed - Tool using the '' | # create a Blast vs. Seed - Tool using the ''create_Blast_vs_SEED_Cluster_Tool.pl'' - script. | ||
# run the tool | # run the tool | ||
# 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> | |||
== 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> | |||
<br> | |||
[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$ClusterTool$ClusterTool_summary.gif]] | |||
<br><br> | |||
== Cluster - Visualisation == | |||
The second part of the result is a visualisation of the clusters. You can see the examined CDS from GenDB and its neighbourhood. You can get more information about each CDS by tooltips. Below you can see the CDS that corresponds to the Blast-hit you used, its neighbourhood and similar clusters in other genomes. Similar colours mean that the CDS are similar (Blast-hits). By clicking a CDS here you are linked to the corresponding entry in the SEED-Database. | |||
<br><br> | <br><br> | ||
[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$ClusterTool$ClusterTool_clusters.gif]] | [[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$ClusterTool$ClusterTool_clusters.gif]] | ||
[[Media:GenDBWiki$$WebDocumentation$$DialogWindows$$ClusterTool$ClusterTool_Bachelorarbeit.pdf]] | === 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. | |||
<br><br> | |||
[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$ClusterTool$ClusterTool_neighbourhood.gif]] | |||
For more information about the Cluster-Tool see [[Media:GenDBWiki$$WebDocumentation$$DialogWindows$$ClusterTool$ClusterTool_Bachelorarbeit.pdf|here]]. | |||
Latest revision as of 07:16, 26 October 2011
Cluster-Tool
The Cluster-Tool can be used to search for conserved gene-clusters. To use the tool you must do the following:
- create a Blast vs. Seed - Tool using the create_Blast_vs_SEED_Cluster_Tool.pl - script.
- run the 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
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: SEED.
File:GenDBWiki$$WebDocumentation$$DialogWindows$$ClusterTool$ClusterTool summary.gif
Cluster - Visualisation
The second part of the result is a visualisation of the clusters. You can see the examined CDS from GenDB and its neighbourhood. You can get more information about each CDS by tooltips. Below you can see the CDS that corresponds to the Blast-hit you used, its neighbourhood and similar clusters in other genomes. Similar colours mean that the CDS are similar (Blast-hits). By clicking a CDS here you are linked to the corresponding entry in the SEED-Database.
File:GenDBWiki$$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.
File:GenDBWiki$$WebDocumentation$$DialogWindows$$ClusterTool$ClusterTool neighbourhood.gif
For more information about the Cluster-Tool see here.