The UCSC Genome Browser has been providing access to reference genomes and associated annotation data for many years now. If you go to the “archives” page you can see the old genomes all the way back to 2003. Check it out–you can find the teeny (but colorful) look at the human assembly from April 2003–and the rather small selection of tracks that were present then. Really–go have a quick look–and realize how much more we have now.
There are new species and new assemblies of the genomes over time, of course. New and updated annotation tracks. New types of tracks–the super-tracks are so loaded with detail and incredibly useful–but are a new concept to grasp. Sometimes tracks get split out–like we’ve seen with the dbSNPs set that now is show as 4 sets instead of the 1 we used to get. Sometimes tracks come back from the past–like the new “Old UCSC Genes” track that just re-appeared on the current human assembly. The paper from the NAR database issue (below) provides a lot of recent highlights.
We’ve been providing training on how to use the features of this browser for many years too. But it certainly has changed over time. We are on version 20 of the intro slides at this point!
This week we are announcing availability of the re-recorded and updated movie, and companion slides and exercises. This focuses mostly on the current human assembly, and includes many of the same basic aspects of organization and function that new users need to understand about the browser. But it also touches on more recent aspects like super-tracks. In this tutorial we don’t cover the track hubs that are referenced in the paper–that’s covered in the recently updated Advanced tutorial with the custom tracks section. And additional details on super-tracks can be found in the ENCODE materials, which are undergoing updates and we’ll be releasing a new version of those materials soon.
As before, you can use the video to teach yourself about the browser features. Or you can use the slides in your lectures or computer labs (the “notes” section contains the things we say on each slide too). You can direct students to the materials too. The materials are all freely available as they are sponsored by the UCSC Genome Browser team.
Many thousands of people have used these movies, slides and exercises over the years to get better acquainted with the browser and tools. And as more data continues to flow in, the more efficient and effective you are with your time and your queries, the faster you’ll get to new discoveries that matter to your work.
UCSC Genome Browser: http://genome.ucsc.edu
Introductory materials: http://openhelix.com/ucsc
Advanced materials: http://openhelix.com/advucsc
Dreszer, T., Karolchik, D., Zweig, A., Hinrichs, A., Raney, B., Kuhn, R., Meyer, L., Wong, M., Sloan, C., Rosenbloom, K., Roe, G., Rhead, B., Pohl, A., Malladi, V., Li, C., Learned, K., Kirkup, V., Hsu, F., Harte, R., Guruvadoo, L., Goldman, M., Giardine, B., Fujita, P., Diekhans, M., Cline, M., Clawson, H., Barber, G., Haussler, D., & James Kent, W. (2011). The UCSC Genome Browser database: extensions and updates 2011 Nucleic Acids Research, 40 (D1) DOI: 10.1093/nar/gkr1055