This week’s tip introduces a nice feature and tool of the Viral Bioinformatics Resource Center (VBRC). There are a lot of great tools at the VBRC to search and analyze hundreds of viral genomes. Most, if not all, of the tools can be used for searching and analyzing bacterial genomes also. The tool we are introducing in this tip is Base by Base. This tip actually came from a question from one of our readers in our weekly “WYP” feature a few weeks back. Reader Azalea asked:
I’m looking for a pairwise sequence alignment tool which can anchor specific nucleotides to be arbitrarily aligned.I just hope to fix certain positions to be aligned, which will change the whole alignment.
Chris Upton at VBRC suggested Base by Base. I’ve had the opportunity to use Base by Base and it’s a useful tool for working with pairwise alignments (could probably be used for any two sequences, not just bacterial and viral) and looks like a tool that Azalea might be able to use. Today’s tip shows you quickly how to add two sequences, align part by hand and select another region to align by algorithm (choice of T-Coffee, ClustalW or MUSCLE).
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.