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).