GenomeViz: visualizing microbial genomes

BMC Bioinformatics. 2004 Dec 15;5:198. doi: 10.1186/1471-2105-5-198.

Abstract

Background: An increasing number of microbial genomes are being sequenced and deposited in public databases. In addition, several closely related strains are also being sequenced in order to understand the genetic basis of diversity and mechanisms that lead to the acquisition of new genetic traits. These exercises have necessitated the requirement for visualizing microbial genomes and performing genome comparisons on a finer scale. We have developed GenomeViz to enable rapid visualization and subsequent comparisons of several microbial genomes in an interactive environment.

Results: Here we describe a program that allows visualization of both qualitative and quantitative information from complete and partially sequenced microbial genomes. Using GenomeViz, data deriving from studies on genomic islands, gene/protein classifications, GC content, GC skew, whole genome alignments, microarrays and proteomics may be plotted. Several genomes can be visualized interactively at the same time from a comparative genomic perspective and publication quality circular genome plots can be created.

Conclusions: GenomeViz should allow researchers to perform visualization and comparative analysis of up to eight different microbial genomes simultaneously.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacterial Proteins / chemistry
  • Bacterial Proteins / classification
  • Bacterial Proteins / genetics
  • Computer Graphics*
  • CpG Islands / genetics
  • Escherichia coli K12 / genetics*
  • GC Rich Sequence / genetics
  • Genes, Bacterial / genetics
  • Genome, Bacterial*
  • Listeria / genetics*
  • Software*
  • Species Specificity

Substances

  • Bacterial Proteins