GenDBWiki/WebDocumentation/DialogWindows/OrthologViewer: Difference between revisions
imported>NilsKleinboelting No edit summary |
m (7 revisions) |
||
| (6 intermediate revisions by one other user not shown) | |||
| Line 4: | Line 4: | ||
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> | ||
| Line 11: | Line 11: | ||
# Use the tool<br> | # Use the tool<br> | ||
<br> | <br> | ||
This is how the window looks like after opening the Ortholog Viewer:<br> | |||
[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$OrthologViewer$ortholog_viewer_1.gif]] | |||
Now you can do the following: | |||
* [[#BrowseOrthologs|Browse through the genome]] | |||
* [[#SelectCDS|Select a CDS]] | |||
You can | [[Anchor(Browse Orthologs)]] | ||
==== Browse through the genome ==== | |||
You can browse through the genome, using the scrollbar. When moving the mouse over a CDS-box, its orthologs are highlighted yellow:<br> | |||
[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$OrthologViewer$ortholog_viewer_2.gif]] | |||
When you find an interesting CDS you may examine it further by selecting it.<br> | |||
<span id=" | <span id="SelectCDS"></span> | ||
==== | ==== Select a CDS ==== | ||
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> | |||
You can | [[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. | |||
Latest revision as of 07:14, 26 October 2011
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? (Points 1-3 are already done, if you prepared the project for the Comparative Annotator
- 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
This is how the window looks like after opening the Ortholog Viewer:
File:GenDBWiki$$WebDocumentation$$DialogWindows$$OrthologViewer$ortholog viewer 1.gif
Now you can do the following:
Browse through the genome
You can browse through the genome, using the scrollbar. When moving the mouse over a CDS-box, its orthologs are highlighted yellow:
File:GenDBWiki$$WebDocumentation$$DialogWindows$$OrthologViewer$ortholog viewer 2.gif
When you find an interesting CDS you may examine it further by selecting it.
Select a CDS
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.
File:GenDBWiki$$WebDocumentation$$DialogWindows$$OrthologViewer$ortholog viewer 3.gif
After selecting a CDS you get a menu:
File:GenDBWiki$$WebDocumentation$$DialogWindows$$OrthologViewer$ortholog viewer 4.gif
You can open the Comparative Annotator or select the chosen CDS in the Main-Window.