Video Tip of the Week: MotifLab workbench for TFBS analysis

When we do workshops, I sing the praises of the ENCODE data that’s genome-wide, and how it is offering amazing new opportunities to explore and discover new features of you genomic regions of interest. But I know that’s all I can do to introduce folks to the data in a short session–and they need to take it to the next level themselves. In the future I’ll be pointing them to MotifLab as a way they might want to proceed after their UCSC and ENCODE training.

MotifLab is a software tool that lets you take segments of interest and process them with a number of other useful data types and tools, integrated into one place. You can then apply various motif finding and analysis tools to assess the region. And you can layer on other data types to help you to further understand what’s going on in that spot.

In the past I might have taken regions of interest from the UCSC Genome Browser and gone to other sites to accomplish many of the things that are integrated into MotifLab. And some of those tools–while nice–don’t offer me the visual track-based additional data I want to consider once I’ve analyzed my stuff. I’d end up taking it back to UCSC as a custom track, uploading that, and then exploring some more. But over many regions, that can be hard to visualize simultaneously.

In fact, it reminds me of a question that a lot of trainees ask in our UCSC Genome Browser workshops: can I have several regions open at the same time? And I think that MotifLab will essentially let you do that, in one place.

They have a series of tutorials to work through to help you to understand what they offer and how to accomplish it. I will point you there, because I haven’t had the time to fully examine all the details myself. But I have plans to take some data I’m interested in, and run it through the paces there. It might not be the right tool for everyone, but it’s got the right combination of tools and graphics to work the way I like to think about the data.

The tutorials they have aren’t embeddable, so I link you to them with the screenshot above. Or you can go directly to the list. They take a while to load, and there’s no audio–you will click through the segments. But they give a good grasp of the kinds of things you can do.

I found out about MotifLab via Chris Upton. Hat tip to his handy Scoop-It collection.

Quick links:

MotifLab: http://www.motiflab.org

MotifLab tutorials list: http://tare.medisin.ntnu.no/motiflab/index.php?page=tutorial

Reference:

Klepper, K., & Drabløs, F. (2013). MotifLab: a tools and data integration workbench for motif discovery and regulatory sequence analysis BMC Bioinformatics, 14 (1) DOI: 10.1186/1471-2105-14-9