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Video Tip of the Week: Send UCSC Genome Browser sequence to external tools

The folks at the UCSC Genome Browser are always adding new features, new data, and new genomes to their site. And although they use the genome-announce mailing list to get the word out, even I can miss a notice. There was news recently of a new feature associated with the graphical genome browser that I’ve been waiting for (as I had tested it prior to roll-out), but they sent the email out when I was prepping for Thanksgiving, and I didn’t catch it for a few days.

But now I’ve had a chance to see it, kick the tires more, and I want to show you how it works. The basic feature is this: you can take the genomic sequence from the window you are viewing and with a couple of clicks deliver it right to another tool for more helpful data or analysis. This is really handy from the graphical viewer. Before you were limited to obtaining the sequence with the “Get DNA” option. You could get the sequence, copy/paste, and do whatever. Which is fine, and might still be right for some other tools. But now you can skip that copy/paste part and explore features of your sequence directly. If you don’t have time for the video, here’s the bullet–use this View–>In External Tools menu to get there.

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There are a range of options. You can still jump right to NCBI Map Viewer or Ensembl to look at the same region in their browsers. But now you can select primers, see restriction sites, look at RNA characteristics, find protein domains, or examine CRISPR tools. You can look for transcription start sites or some TF binding motifs. Here’s this week’s Video Tip that shows the process.

You can still “get DNA” if you want to. And you can still use the Table Browser to send data from your custom queries to even more tools (like Galaxy and others). But we know from our workshops that most people we train spend their time in the graphic browser and these tools should help them accomplish more. You can see all of these options in our freely available training suites (linked below).

To see if there are other things you missed over the past year, check out the new NAR database issue paper from the UCSC team (linked below). It has updates about many of their accomplishments and recent features, so have a look and see if there are other useful aspects for assisting your research.

Quick links:

UCSC Genome Browser:

Intro full training suite:

Advanced topics training suite:


Speir, M., Zweig, A., Rosenbloom, K., Raney, B., Paten, B., Nejad, P., Lee, B., Learned, K., Karolchik, D., Hinrichs, A., Heitner, S., Harte, R., Haeussler, M., Guruvadoo, L., Fujita, P., Eisenhart, C., Diekhans, M., Clawson, H., Casper, J., Barber, G., Haussler, D., Kuhn, R., & Kent, W. (2015). The UCSC Genome Browser database: 2016 update Nucleic Acids Research DOI: 10.1093/nar/gkv1275

Disclosure: UCSC Genome Browser tutorials are freely available because UCSC sponsors us to do training and outreach on the UCSC Genome Browser.