A project I've been working on for the last two months is finally online in beta form - check out

http://rcat.codeplex.com/

It's essentially a biological alignment viewer for RNA sequences.  Here's a couple of screen shots:

Alignment Viewer

2D Structure Viewer

2D Circle relationship Viewer

You can download the source code from the above link to play with it - it's a MVVM implementation and has quite a bit of interesting optimizations in it for performance purposes, including a read-only data virtualization for large sequence manipulation.  The next release will include a full read/write implementation so watch the project if you are interested!