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GenomeViz: visualizing microbial genomes.

Ghai R, Hain T, Chakraborty T

Institute of Medical Microbiology, Faculty of Medicine, Justus-Liebig-University, Frankfurter Strasse 107, D-35392 Giessen, Germany. Rohit.Ghai@mikrobio.med.uni-giessen.de

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.

Published 11 January 2005 in BMC Bioinformatics, 5(1): 198.
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