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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Bring your questions, comments and suggestions to WormBase staff at IWM 2023!

WormBase is excited and looking forward to being in Glasgow for IWM 2023! We have many activities scheduled including a plenary talk in the evening on June 24th, the WormBase workshop in the afternoon of June 25th which will present and discuss data and tools in WormBase and the Alliance of Genome Resources, and the WormBase and microPublication booth that will be open from June 25th to June 27th. Come visit us with your questions, comments and suggestions at any of these occassions, we’d be happy to talk to you!

Three more days to contribute to WB community curation to WIN PRIZES at the IWM in Glasgow!

You have 3 more days to make it to the top 10! Submit your data now, the deadline for submission is June 10th, 2023. The top submitter (Paul Sternberg, excluded!) will win a voucher for a microPublication ($250 value!). Additional prizes will be awarded at the WormBase booth. Access the submission forms here.