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 | 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> | ||
# 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'' (there will be a script for this soon)<br> | |||
# Run ''set_biderectional_project_config.pl''. Now the "Comparative Region Annotation"-Button is shown, when a CDS is selected<br> | |||
# Use the tool<br> | |||
<br> | <br> | ||
== 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 | 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 | On the right side of the image you can do the following: | ||
* [[#AnnotateReference|Annotate the Reference]] | |||
* [[#CopyAnnotation|Copy Annotation]] | |||
* [[#ViewMultipleAlignment|View multiple alignment]] | |||
<span id="AnnotateReference"></span> | |||
==== Annotate the reference ==== | ==== Annotate the reference ==== | ||
You can select one CDS as reference and annotate it (or check if | 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> | |||
- click the '''"Annotate Reference"''' - button<br> | |||
- do your annotation<br> | |||
[[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$ComparativeAnnotator$compAnno_annotateReference.gif]] | [[Image:GenDBWiki$$WebDocumentation$$DialogWindows$$ComparativeAnnotator$compAnno_annotateReference.gif]] | ||
==== Copy | <span id="CopyAnnotation"></span> | ||
==== Copy Annotation ==== | |||
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 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 '''"OK"'''<br> | |||
[[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> | |||
==== 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 == | ||
<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 1.0*e-10, red arrows indicate Blast hits with an e-value greater then 1.0*e-10.<br> | |||
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> | |||
[[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><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 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]] | ||
Latest revision as of 21:06, 15 November 2011
Comparative Annotator
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.
What should be done to use this tool?
- create Bidirectional-Blast-Tools in the project with: create_genome_compare_tools.pl
- Run the Tool for each Contig-combination with: submit_job.pl (there will be a script for this soon)
- Run set_biderectional_project_config.pl. Now the "Comparative Region Annotation"-Button is shown, when a CDS is selected
- 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 information about the CDS by tooltips.
File:GenDBWiki$$WebDocumentation$$DialogWindows$$ComparativeAnnotator$compAnno part1.gif
On the right side of the image you can do the following:
Annotate the reference
You can select one CDS as reference and annotate it (or check if the annotation is correct), using the Annotation Dialog.
- select the desired CDS as Reference
- click the "Annotate Reference" - button
- do your annotation
File:GenDBWiki$$WebDocumentation$$DialogWindows$$ComparativeAnnotator$compAnno annotateReference.gif
Copy Annotation
You can copy the annotation from one CDS to others.
- select the CDS with the annotation you want to copy as Reference
- select the CDSs where you want the annotation to be copied as Annotate
- click the "Copy Annotation" - button
File:GenDBWiki$$WebDocumentation$$DialogWindows$$ComparativeAnnotator$compAnno copyAnnot1.gif
- when you are sure that you want to copy the annotation, click "OK"
File:GenDBWiki$$WebDocumentation$$DialogWindows$$ComparativeAnnotator$compAnno copyAnnot2.gif
- The annotations are now copied
View multiple alignment
You can compute a multiple Alignment of two or more CDS with ClustalW.
- choose two ore more CDS with the "mult. Alignment"-Checkboxes
- click the "View multiple alignment"-button
- wait for the result
File:GenDBWiki$$WebDocumentation$$DialogWindows$$ComparativeAnnotator$compAnno multAlign.gif
CDS Comparison
The second part of the window shows Blast-Hits between the detected CDS. Green arrows indicate a Blast hit with an e-value smaller then 1.0*e-10, red arrows indicate Blast hits with an e-value greater then 1.0*e-10.
On the right side of the image you get some information about the selected CDS. By clicking on a CDS you can select others.
File:GenDBWiki$$WebDocumentation$$DialogWindows$$ComparativeAnnotator$compAnno part2.gif
View aligment
You can have a look at an alignment by clicking on an arrow and selecting "Result"
File:GenDBWiki$$WebDocumentation$$DialogWindows$$ComparativeAnnotator$compAnno alignment.gif
Other similar CDS
Under "Other similar CDS" in the detail-view of a CDS you can see some other good Blast Hits. By clicking them you can call the Comparative Annotator for that CDS.
File:GenDBWiki$$WebDocumentation$$DialogWindows$$ComparativeAnnotator$compAnno otherSimilar.gif
