Got a genome? Need a browser?
From the GBrowse mailing list the other day came notice of a new way to use GBrowse–without programming! A team from Indiana University has lowered the barrier of entry for anyone with a genome they want to display. They have created an interface and web server for GBrowse that lets you simply upload your data and make some choices for the display…and voilà! You have a genome browser. It is called WebGBrowse, and I think it is tremendously helpful. http://webgbrowse.cgb.indiana.edu
As we push forward with more and more sequence data for anyone’s favorite species, and with personal genomes, a rapid and programming-lite option for examining this data needs to exist. This is a step in that direction. All you need to do is get your data into GFF3 format (and they give you a sample), you upload it, you pick some display features, and you can be looking at your genome and annotation features in no time at all.
Even if you decide you wanted to build the standard GBrowse version it would be really helpful for the team to mock it up in the WebGBrowse interface to discuss the features. It might also be an nice way to get students thinking about such displays and then take them over to the regular GBrowse tools. I could also see creating displays for your gene of interest with various features that are important for your work, or to display for presentations and papers. I wonder if there is a lower size limit to what you can display…hmm….
I used their sample file to upload and examine and it was very neat and dramatically quick. I’m going to try to edit that GFF with some sample data that I’ll pull out of NCBI–just to try it out. One thing that would make my life just that much easier would be to use the GFF file as a web form so I could just load data in that way. I can see the need for uploading some things (like lists of genes or primers or variations) and I would want a way to save the output for re-upping and sharing, but I would love to be able to handle each of those separately instead of one big GFF. Another handy feature would be to be able to load a GenBank format file right up. I wonder if there is a web converter out there for that (I know it exists on the programming side)…I’ll have to look. Or let me know in the comments if you have one. But these are minor enhancement requests–it seems to work great already. And maybe I’ll learn more as I spend a bit more time with it.
If you are totally new to GBrowse you might want to have a look at our free tutorial on it. Dozens of research groups are using GBrowse to display their data now, and more are coming along all the time. It will help you to understand the structure and the kinds of things you can expect–and envision what you want to display.
Anyway–congrats to the team that created WebGBrowse. I think it will be really useful in many ways. And it is lifting the burden for biologists that don’t have programming resources–that is seriously helpful.
More like this, please
Podicheti, R., Gollapudi, R., & Dong, Q. (2009). WebGBrowse – a web server for GBrowse Bioinformatics DOI: 10.1093/bioinformatics/btp239