GenDBWiki/WebDocumentation/DialogWindows/ComparativeAnnotator: Difference between revisions
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= 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. | 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> | ||
<br> | |||
What should be done to use this tool? | What should be done to use this tool?<br> | ||
1. create [[BiDir]]-Blast-Tools in the project with: create_genome_compare_tools.pl | 1. create [[BiDir]]-Blast-Tools in the project with: create_genome_compare_tools.pl<br> | ||
2. Run the Tool for each Contig-combination with: submit_job.pl (there will be a script for this soon) | 2. Run the Tool for each Contig-combination with: submit_job.pl (there will be a script for this soon)<br> | ||
3. Run set_biderectional_project_config.pl. Now the "Comparative Region Annotation"-Button is shown, when a CDS is selected | 3. Run set_biderectional_project_config.pl. Now the "Comparative Region Annotation"-Button is shown, when a CDS is selected<br> | ||
4. Use the tool | 4. Use the tool<br> | ||
<br> | |||
== Genome View == | == Genome View == | ||
Revision as of 17:28, 3 March 2006
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.
What should be done to use this tool?
1. create BiDir-Blast-Tools in the project with: create_genome_compare_tools.pl
2. Run the Tool for each Contig-combination with: submit_job.pl (there will be a script for this soon)
3. Run set_biderectional_project_config.pl. Now the "Comparative Region Annotation"-Button is shown, when a CDS is selected
4. Use the tool
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.
File:GenDBWiki$$WebDocumentation$$DialogWindows$$ComparativeAnnotator$compAnno part1.gif
On the righten side of the image you can do the following:
Annotate the reference
File:GenDBWiki$$WebDocumentation$$DialogWindows$$ComparativeAnnotator$compAnno annotateReference.gif
Copy Annotations
File:GenDBWiki$$WebDocumentation$$DialogWindows$$ComparativeAnnotator$compAnno copyAnnot1.gif
File:GenDBWiki$$WebDocumentation$$DialogWindows$$ComparativeAnnotator$compAnno copyAnnot2.gif
View multiple alignment
File:GenDBWiki$$WebDocumentation$$DialogWindows$$ComparativeAnnotator$compAnno multAlign.gif
CDS Comparison
File:GenDBWiki$$WebDocumentation$$DialogWindows$$ComparativeAnnotator$compAnno part2.gif
View aligment
File:GenDBWiki$$WebDocumentation$$DialogWindows$$ComparativeAnnotator$compAnno alignment.gif
Other similar CDS
File:GenDBWiki$$WebDocumentation$$DialogWindows$$ComparativeAnnotator$compAnno otherSimilar.gif
