JBrowse plugin to view the sequence of features
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README.md

README.md

##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" ],
    ```
    
  1. 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.