FeatureSequence

FeatureSequence is a plugin built for the genome browser JBrowse.

It provides the user with a quick interactive tool for viewing the sequences of various features.

FeatureSequence allows the user to:

• Toggle the display of different types of subfeatures

  • Introns are automatically assumed from exon boundaries
  • Easily retrieve spliced CDS

• Highlight any type of subfeature in a randomly selected pastel color

  • Highlights are preserved if copied into a rich text editor (MS Word, LibreOffice Writer, etc.)

• Change case of any type of subfeature

  • Can be used to map intron/exon junctions
  • Simplify RealTime qPCR primer design

• View upstream and downstream sequences

To use the FeatureSequence plugin:

1. Clone this repository into your jbrowse/plugins/ directory

   git clone https://github.com/tsaari88/FeatureSequence
   

2. Add the plugin to your JBrowse configuration as described in the JBrowse configuration guide.

• e.g. editing jbrowse_conf.json:

  ```
  "plugins": [ "FeatureSequence" ],
  ```
  

3. Finally, you must add a way to call FeatureSequence. For example, you want to add a right-click menu option to launch FeatureSequence on your favorite Example_Track. Do this by editing trackList.json, adding the menuTemplate value to the track labeled "Example_Track":

            "key" : "The best genes ever",
            "label" : "Example_Track",
            "menuTemplate" : [
               {},
               {},
               {
                  "content" : "function(track,feature){return track.browser.plugins.FeatureSequence.callFxn(track, feature); }",
                  "label" : "View Feature Sequence",
                  "action" : "contentDialog",
                  "iconClass" : "dijitIconBookmark"
               }
            ],
   
            ...
   

Now in JBrowse, when right-clicking a feature on Example_Track, you will have the option to "View Feature Sequence." This will open up a Feature Sequence Viewer pop-up dialog with interactive features for a customized sequence view.

Additional Details

FeatureSequence Author: Travis Saari.

In creating the plugin, I borrowed a lot of concepts and code from a similar plugin called SeqLighter, which can be found at this link.

I have added the hide/show and text-case-change functionalities, as well as completely re-worked the code to run asynchronously and to eliminate dependencies - dojo functions were utilized rather than jQuery functions, and a stand-alone viewer module was created. I believe that this plugin will provide some much-desired functionality to JBrowse.