Base-By-Base: Single nucleotide-level analysis of whole viral genome alignments

Background: With ever increasing numbers of closely related virus genomes being sequenced, it has become desirable to be able to compare two genomes at a level more detailed than gene content because two strains of an organism may share the same set of predicted genes but still differ in their pathogenicity profiles. For example, detailed comparison of multiple isolates of the smallpox virus genome (each approximately 200 kb, with 200 genes) is not feasible without new bioinformatics tools. Results: A software package, Base-By-Base, has been developed that provides visualization tools to enable researchers to 1) rapidly identify and correct alignment errors in large, multiple genome alignments; and 2) generate tabular and graphical output of differences between the genomes at the nucleotide level. Base-By-Base uses detailed annotation information about the aligned genomes and can list each predicted gene with nucleotide differences, display whether variations occur within promoter reg...

• Type: Journal
• Year: 2004
• Where: BMCBI
• Authors: Ryan Brodie, Alex J. Smith, Rachel L. Roper, Vasily Tcherepanov, Chris Upton
• Keywords: Aligned Genomes, Annotation Information, BMCBI 2004, Genomes