Video Tip of the Week: UCSC Genome Browser restriction enzyme display

We often like to highlight new resources in our tips of the week to show people about some new way to find, explore or analyze genomic data. But sometimes we also want to point out a new aspect of a resource we’ve seen before, or highlight some feature that people tell us they were wondering about. Lately I noticed a number of searches to our blog about viewing restriction enzymes in the UCSC Genome Browser. So I decided it was time to illustrate that.

In this week’s tip I point out where to find the restriction enzyme data track. The choices for the display of that data are shown. And we explore the track details page to learn more about the track source and properties. We’ll see that the track relies on REBASE, the restriction enzyme database from New England Biolabs, and we’ll see some of the display aspects that you should know about. I’ll show how to filter the REBASE data to show only one specific enzyme too.

This track has been around for a while, but I think a lot of people don’t realize it is there or how to use it. If you want more details about other features of the browser including some of the latest developments you should check out the recent publication from the UCSC team in the NAR database issue. There may be more tracks that you aren’t aware of yet that could help you to accomplish your research goals.

One of the other very exciting things in that paper was the note that they will be offering a way for people with assembly data that is not deposited at NCBI to use the browser and tools:

Many researchers have expressed interest in using the Genome Browser to visualize and analyse assemblies that are not deposited at NCBI. To assist such research, we intend to develop support for assembly data hubs, which will enable the genomics community to easily extend the Genome Browser to display genome assemblies that we are unable to integrate into our own database.

That’s a question we hear a lot at workshops lately: what’s the easiest way to use the UCSC genome browser for my genome of interest? This sounds like a terrific opportunity for that.

If you want a more complete exploration about the organization and visualization features of the UCSC Genome Browser, you should have a look at the full introductory tutorial: openhelix.com/ucsc . This tutorial is freely available because it is sponsored by the UCSC Genome Browser team. There’s a full video, slides, and exercises you can download and use to train yourself or others.

Quick links:

UCSC Genome Browser Restriction Enzyme track: cutters

REBASE: http://rebase.neb.com

References:

Meyer, L., Zweig, A., Hinrichs, A., Karolchik, D., Kuhn, R., Wong, M., Sloan, C., Rosenbloom, K., Roe, G., Rhead, B., Raney, B., Pohl, A., Malladi, V., Li, C., Lee, B., Learned, K., Kirkup, V., Hsu, F., Heitner, S., Harte, R., Haeussler, M., Guruvadoo, L., Goldman, M., Giardine, B., Fujita, P., Dreszer, T., Diekhans, M., Cline, M., Clawson, H., Barber, G., Haussler, D., & Kent, W. (2012). The UCSC Genome Browser database: extensions and updates 2013 Nucleic Acids Research, 41 (D1) DOI: 10.1093/nar/gks1048

Roberts, R., Vincze, T., Posfai, J., & Macelis, D. (2009). REBASE–a database for DNA restriction and modification: enzymes, genes and genomes Nucleic Acids Research, 38 (Database) DOI: 10.1093/nar/gkp874

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  1. Pingback: Video Tip of the Week: UCSC Genome Browser restriction enzyme display | DNAresearch | Scoop.it

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