Recently in a paper we are working on we were asked to cover a bit more about various styles or types of genome browsers that are available. And the timing was perfect, because I had just revisited the information about IGB (Ig-bee) in their recent webinar series.
Announced on Biostar recently was this nice introduction to the new version: Live tour of new features in Integrated Genome Browser 8. Although I missed the live webinar, you can catch various recordings from their YouTube channel. I watched the intro one, but it doesn’t seem to be available right now (I’ve asked for a new link over at Biostar). It was a nice overview of the site, with an introduction to their setup and basic features. I’m hoping that it will re-appear soon. In the meantime, their YouTube page offers a few other ways to get started with IGB. Here’s one video, but there are several other quick-start style ones.
One of the key aspects was this nice way for groups to collaborate on evaluation and annotation of their data:
IGB makes it easy for groups to distribute and share their new genome assemblies and annotations. Using IBG’s simple QuickLoad system, you can share your new genome with collaborators, keeping the data private until published, and then use the same method to share the data with the world.
And there’s a lot more you can do. But that should give you a sense of the utility.
I played with IGB’s current version, and found it very flexible and useful. I may have overburdened it by asking for all those restriction sites, but they eventually loaded. I also loaded up some of the UCSC Genome Browser external data. You’d have to be familiar with the names of the data sets you’d want from UCSC beforehand though–a trip through our Table Browser tutorial might help you to understand that aspect a bit better. But sometimes the big public genome browser sites won’t have all the flexibility and customization that you want for your explorations–and adding a browser like IGB to your repertoire could really help you to get precisely what you need in your data analysis projects.
IGB site: http://bioviz.org/igb/
YouTube channel with more videos: IGB Channel
Nicol J.W., Helt G.A., Blanchard S.G., Raja A. & Loraine A.E. (2009). The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets, Bioinformatics, 25 (20) 2730-2731. DOI: 10.1093/bioinformatics/btp472