Video Tip of the Week: Viewing Amino Acid info in the UCSC Genome Browser

We’ve been doing training on the UCSC Genome Browser for over 10 years now. We’ve seen it grow from just a few genomes and a few tracks to the enormous trove of information it is today. In fact, one of the toughest things about training is how to balance all the new information and features with the foundational things one needs to really grok the framework and the functionality.

ucsc_aminoacidsIn the training materials that we have today, we touch briefly on the amino acid display in the reference genome track. And one of our very first Tip-of-the-Week blog posts was about how to visualize the 3-frame translation on the browser. But we don’t have time to go into every track and show the options that you can employ for all the displays. We stress that you should check each track for more features, but in the short workshops we can only cover a few examples.

The UCSC team has started a great video series that can supplement the main training  suites that are available. You can see their whole YouTube channel here: UCSC Genome Browser. But today I’ll highlight one of the recent ones so you can see the type of help they offer. And it covers a feature–display of amino acids, codon numbers, and amino acid variation information, that we don’t have time to do in our workshops.

How do I identify codon numbers with the UCSC Genome Browser?

Bob Kuhn and Pauline Fujita’s video here, as well as the others in the series, focus on a specific task and give great tips and details. Be sure to check out the others as well, and subscribe to their channel to be notified when new ones become available.

Quick links:

UCSC Genome Browser: http://genome.ucsc.edu

UCSC YouTube Channel: http://bit.ly/genomebrowserYoutube

OpenHelix full training suite materials:

Note: UCSC has sponsored our training materials for years, and because of this sponsorship they are freely available to everyone.

Reference:

Rosenbloom K.R., J. Armstrong, G. P. Barber, J. Casper, H. Clawson, M. Diekhans, T. R. Dreszer, P. A. Fujita, L. Guruvadoo, M. Haeussler & R. A. Harte & (2014). The UCSC Genome Browser database: 2015 update, Nucleic Acids Research, 43 (D1) D670-D681. DOI: http://dx.doi.org/10.1093/nar/gku1177