For this week’s Tip of the Week, I’m going to highlight a tool that I think is very necessary. In fact, more than once we’ve had folks in workshops ask for something like this. I hope that some people will try this out and see if it solves their problem of having so many interesting regions to explore. Have a look at the MIG, or Multi-Image Genome Database. Right on the top of their page they nailed the issue:
We have developed a software tool to visualise genomic data based on popular web-based genome browsers such as GBrowse and UCSC. While web browsers excel at the display of disparate data at a single locus, it can be time-consuming to compare this data with that of other genomic loci.
Now, this is, of course, a good problem to have. You want to look at multiple locations in a genome for related genes, pathway members, and more. Maybe you want to assess the promoters, or chromatin structure, or whatever–but you may need to examine several of them visually and get a sense if there’s some pattern or relationship to the signals they might share. Or maybe you want to confirm very different natures that they might have. But having a quick way to load up new segments and have a look could really help. Then you can take this further with filtering, querying, and sorting options.
This resource isn’t brand new, but I’m highlighting it because of a new paper that they’ve just published. You can learn more about their philosophy and strategies there (it’s linked at the bottom). But they also did videos that will help you get to know MIG. You’ll find links to them on their handy Tutorials and Help page, and you’ll see other things you might want to use such as the step-by-step written guides for common tasks, and some useful files in the “accessory scripts” area that they provide.
Here I’ll highlight one of their videos, but you can learn more on their Help page.
I picked this video because it gives you a sense of what you can do once your data is loaded in. Another video covers how to get your data into the database. But as I mentioned, there’s even more help and guidance in their paper and their documentation. Check it out.
McGowan S.J., Hughes J.R., Han Z.P. & Taylor S. MIG: Multi-Image Genome Viewer, (2013). Bioinformatics, DOI: 10.1093/bioinformatics/btt406