VARNA (Visualization Applet for RNA) (http://varna.lri.fr/) is a new tool for RNA secondary structure visualization and it has a lot going for it: open source, pretty structure rendering, export to svg/jpg/eps, interactive inspection of structure with change of layout algorithm (linear/circular/radial). And most importantly: it is so simple to use that it is actually practical! If you are a teacher/student in a class covering RNA structure you should really have a closer look at VARNA. As a researcher, it is very easy to store dynamic VARNA-enabled RNA secondary structures on your computer – and in some situations this is really what you want.

The Center for Bioinformatics at University of Hamburg recently published, and made available, a C library for plotting genomic data. Furthermore, they also provide Python, Ruby and Lua bindings to their library. Check it out here.

Also, if you use Ruby you might want to check out Bio::Graphics for visualizing genomic data.