Last fall I noticed an announcement at Biostar about an upcoming webinar that would illustrate some new features in the IGB browser. And at the time I highlighted some of their materials as our video tip that week. So for more details you can check out that overview.
But recently I was told that their longer-form introduction is available again. If you are interested in the different functionalities of various browsers this is a better overview perhaps. So now that it’s viewable again I thought I’d offer that as the tip this week. It’s in 2 parts, the first one is here:
The second one is available with the other videos on their YouTube channel: Introduction to IGB Part II: Starting Analysis.
To get an idea of how it’s used in the field, have a look at data about blueberries. There’s a SlideShare of Ann Loraine’s recent presentation that shows you where to find their blueberry RNA-Seq data. On slide 13 there’s a neat example of the different transcripts present in ripe and unripe fruit. With those details (focusing on Cuff.187.1 region, and loading up the RNA-Seq Berry Development tracks, load the “coverage” files in the Graphs folder) I was able to see exactly what they show as the difference among the data sets. And I loved how they were color-coded to match the berry stages–I thought that was very effective. The slides go on to show further steps of annotation and exploration with Blast2GO and PlantCyc. And they show some sample data of pathways that are altered over developmental time points.
So have a look at IGB, and the great example of how it can be used to visualize key features in genomic data. And have some blueberries.
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