Base-By-Base version 2: single nucleotide-level analysis of whole viral genome alignments

In version 2, BBB-v2, of Base-By-Base we have added a series of new features aimed at providing the bench virologist with a better platform to view, annotate and analyze these complex genomes. Although a poxvirus genome, for example, may be less than 200 kb, it probably encodes close to 200 proteins using multiple classes of promoters with frequent overlapping of promoters and coding sequences and even some overlapping of genes. The new features allow users to 1) add primer annotations or other data sets in batch mode, 2) export differences between sequences to other genome browsers, 3) compare multiple genomes at a single nucleotide level of detail, 4) create new alignments from subsets/subsequences of a very large master alignment and 5) allow display of summaries of deep RNA sequencing data sets on a genome sequence.BBB-v2 significantly improves the ability of virologists to work with genome sequences and provides a platform with which they can use a multiple sequence alignment as the basis for their own editable documents. Also, a .bbb document, with a variety of annotations in addition to the basic coding regions, can be shared among collaborators or made available to an entire research community. The program is available via Virology.ca using Java Web Start and is platform independent; the Java 1.5 virtual machine is required.The original version of Base-By-Base (BBB) [1] was developed by the Virus Bioinformatics Resource Center primarily because of a need for a customizable, platform-independent (Java), multiple sequence alignment (MSA) editor that could be used for the comparison, annotation and analysis of viral genomes, and also integrated directly with our MySQL database. There are now several somewhat related MSA tools; however, each has their own set of distinctive features that make them especially valuable in their niche environments. For example, JalView [2] and STRAP [3] focus on features for display and analysis of proteins, whereas SeaView [4] add