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:

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JBrowse 2: Getting Sequence

In JBrowse 2 there are multiple ways to obtain sequence information. One is via a context menu when region is selected by clicking and dragging on the “number line” part of the linear genome view:

Selecting “Get sequence” from the context menu will open a dialog where you will have a few options for how to get your sequence:

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WS286 genome browser

The new genome browser software is a live, in-page genome browser that you can add tracks to, pan, zoom and do a variety of things JBrowse 1 could do without leaving the page. If you’d like a full page JBrowse 2, you can click on the link just above the genome browser, or if you’d like to use JBrowse 1, you can click on the “Legacy” link just below JBrowse 2 to get the old JBrowse 1 image and link back. Please let us know if you have any comments or questions by writing to help@wormbase.org.