Base-By-Base version 2 : single nucleotide-level analysis of whole viral genome alignments
Date
2011-06-14
Authors
Hillary, William
Lin, Song-Han
Upton, Christopher
Journal Title
Journal ISSN
Volume Title
Publisher
BioMed Central
Abstract
Background: Base-By-Base is a Java-based multiple sequence alignment editor. It is capable of working with
protein and DNA molecules, but many of its unique features relate to the manipulation of the genomes of large
DNA viruses such as poxviruses, herpesviruses, baculoviruses and asfarviruses (1-400 kb). The tool was built to serve
as a platform for comparative genomics at the level of individual nucleotides.
Results: 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.
Conclusion: 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.
Description
BioMed Central
Keywords
Citation
Hillary et al.: Base-By-Base version 2: single nucleotide-level analysis of whole viral genome alignments. Microbial Informatics and Experimentation 2011 1:2.