Tag Archives: gbrow

Tip of the week: Sol Genomics Network

sol_genomics_networkAside from a short stint at the ASHG meeting, where it is all about the human genome with a smidge of attention to the microbes that hang around with us, I’m back and I’m focusing on plant resources again.  Recently I began to explore the Sol Genomics Network site, and that will be the focus of this tip of the week.

Sol Genomics Network focuses on “Solanaceae as model system for diversity” as they describe themselves.  And they aim to link genotypes to phenotypes for a collection of plant species.  Currently species information found at this site include: tomato, potato, eggplant, pepper, petunia, tobacco, and coffee.  Not all of them have browsers available here, but there are some maps for several, and there are links to other sources that may provide more information about the projects, clone collections, and additional details. They are also developing a breeder’s toolbox and they’d like to have some feedback on the needs of the community on that.

We will take a look at their tomato browser today, which is implemented in GBrowse, the Generic Genome Browser from the GMOD project tool kit that supports so many species and data types–and if you want some help using GBrowse you should see our freely available tutorial on that.

The site also include a number of outreach activities for students at varying levels–including a lab exercise for the high school level, a word find puzzle for youngsters with these species (we like puzzles here), and the fun and interactive animated series with a sequencing puzzle where you generate a small assembly with some sample BAC fragments (ok, they are really small BACs, but you get the point).   I know a lot of, ah, mature scientists who could stand to work with the concept of the assembly to grok that a bit better, actually….

Go directly to the BAC assembly sequencing puzzle here if you don’t have time for the whole tip of the week:  http://bti.cornell.edu/multimedia/puzzleComplete.html

Sol Genomics Network site directly: http://solgenomics.net/

More Solanaceae resources: http://solanaceae.plantbiology.msu.edu/