Can I read Base-By-Base version 2: single nucleotide-level analysis of whole viral genome alignments on EtoBox?

Base-By-Base version 2: single nucleotide-level analysis of whole viral genome alignments by William Hillary; Song-Han Lin; Chris Upton is a scholarly article available to read on EtoBox.

What is Base-By-Base version 2: single nucleotide-level analysis of whole viral genome alignments about?

## 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 summar

Author

William Hillary; Song-Han Lin; Chris Upton

Publisher

BioMed Central; Springer (Biomed Central Ltd.); BioMed Central Ltd.; London: BioMed Central; Springer Science and Business Media LLC (ISSN 2042-5783)

Published

2011

Language

EN