I just spent a bit over an hour getting some one-on-one time with Chris Upton at Viral Bioinformatics Resource Center. He was showing me the tools and resources they have (we used the new screensharing iChat feature of Leopard OS 10.5, that alone was worth the cost of upgrading to 10.5 this week, or even dumping your PC and getting a Mac ;-)… but I digress…) and they look quite useful. You can analyze a large number of viral genomes in their database (or upload your own, or a bacterial genome for that matter) in many different ways. Their webpage navigation and look is going to change soon (and I’ll inform you when it does), but the software and tools will remain the same (they are mainly Java programs), so if you want, you can go check them out. I suggest starting with VOCS which is a sort of an advanced search/filter/browser for viral genomes and from which you can access several other of the tools. We’ll be looking at these tools more in depth (I have a couple tips planned for the near future, tutorial), but thought I’d point it out to you now. Quite nice.