Monday, October 12, 2009

Next Generation Genome Browser

When David, Fang Fang and I talk about UCSC Genome Browser today, I said "I would like a genome browser like Google Map". Later I find I become more excited about this idea: the next generation genome browser, which provides an more user friendly and powerful platform to ornanize and display genomic information.

What does the next genome browser ("genome map") look like ?

First, smoother zoom in and zoom out. Genomes are organized in hierarchical structure. Sometimes we need a birdview of the whole genome and sometimes we are interested in subtle local structures. It is of great value if we are change the resolution when examining the genome. So, we need dynamic and smoother zoom in and zoom out just like the little sliding bar in Google map. (update: I came across Jbrowser and Anno J browser that seems to have this function. See reference)

Second, advanced searching functions. Current genome browser are only able to search by genomic location, as a result the vast amount of annotation information can not be searched in genome browser. It will be cool there is a search box. Users input a keyword , such as a gene name and the our genome map display those regions match the query.

Third, what kind of web technology should we need? Ajax? Database back end? XML? Maybe google map is a good starting point.

There seems great possibility that such a genome map will appear and what other features are you looking for in the next generation genome brower?

1. Skinner ME, Uzilov AV, Stein LD, Mungall CJ, Holmes IH. JBrowse: A next-generation genome browser. Genome Res. (2009)
2. AnnoJ Browser