JBrowse 2: Searching for features and sequences

Searching in JBrowse 2 is quite similar to searching in JBrowse 1. The most common way you would look for a feature would be to type the name of a feature in the location field (that is, the field that has the current location in it, like this:

Anything that you could search for in JBrowse 1 you can search for in JBrowse 2, and there is a good reason for that: they are using exactly the same data and search indexes. So, you can look for gene and transcript names, identifiers like WBGene00006749, and allele names like pkP649.  Of course, you can also enter a location like II:100000..200000. The only difference in name searching between JBrowse 1 and 2 is that when you search for something, you will almost always get a message like this in the bottom of the screen:

This message can be ignored. It results from the sharing of data between JBrowse 1 and 2 and occurs because JBrowse 2 wants to open the track where the feature was found, but because it isn’t possible for JBrowse 1 and 2 to share track identifiers, this will not be easy to fix. Nevertheless, we hope to have this message removed in a future release of WormBase.

Searching for sequence is similar in JBrowse 2 as well. In the “hamburger menu” in the upper left corner of a linear genome view, there is a sequence search option:

Selecting it will open a search dialog, with options to add the sequence you’re looking for and to indicate strand if necessary and to make it case insensitive (generally speaking, at WormBase, I think you’ll always want a case insensitive search).  Additionally, note that you can use regular expressions in your search, so for example, having a question mark after a character means it’s optional and putting several characters inside of square brackets means that any one of those is acceptable in that position. Here’s an example search and result:

Note that search results like this will remain in JBrowse as long as the session is active (basically, until you close the window), but sessions can be saved and reopened (see the help document on that topic). Also note, that as with most things in these help docs, anything described here can be done in both the JBrowse web app as well as the JBrowse that is embedded in many WormBase windows.

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