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
Highlight any type of subfeature in a randomly selected pastel color
Change case of any type of subfeature
View upstream and downstream sequences
Clone this repository into your jbrowse/plugins/ directory
git clone https://github.com/tsaari88/FeatureSequence
Add the plugin to your JBrowse configuration as described in the JBrowse configuration guide.
e.g. editing jbrowse_conf.json:
"plugins": [ "FeatureSequence" ],
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.
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.