GenomeViz: visualizing microbial genomes - PubMed (original) (raw)

Comparative Study

GenomeViz: visualizing microbial genomes

Rohit Ghai et al. BMC Bioinformatics. 2004.

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.

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Figures

Figure 1

Figure 1

Whole genome alignments of five Listeria strains/species. From outside to inside: L. monocytogenes EGDe serovar 1/2a COG categories (outer two circles), L. monocytogenes F6854 serovar 1/2a (blue, 133 contigs), L. monocytogenes F2365 serovar 4b (red, whole genome), L. monocytogenes H7858 serovar 4b (orange, 180 contigs) and L. innocua (innermost, green, whole genome). All genomes were aligned separately to L. monocytogenes EGDe with AVID. Sequence data for strains L. monocytogenes strains F6854 and H7858 was obtained from The Institute for Genomic Research [17].

Figure 2

Figure 2

A typical image generated by GenomeViz. From outside to inside: Listeria monocytogenes COG categories (two circles), horizontally transferred gene categories in L. monocytogenes identified using SIGI (two circles), mean centered GC% of L. monocytogenes genes (red-above mean, blue-below mean, one circle), GC% gradient (red-high GC%, green-low GC%, one circle), Listeria innocua COG categories (two circles), horizontally transferred gene categories in L. innocua identified using SIGI (two circles), mean centered GC% of L. innocua genes (red-above mean, blue-below mean, one circle), GC% of L. innocua genes shown as a line graph (innermost circle). When created in GenomeViz, this image is fully interactive and any plotted circle may be queried. It also shows the different ways in which qualitative or numerical data may be plotted. Differences in the horizontally transferred genes in the two Listeria species may be examined and related to GC content in the region.

Figure 3

Figure 3

**Comparing data from different sources using GenomeViz.**The figure shows a comparison of the distribution of horizontally transferred genes in Escherichia coli K12 compiled from three different sources. From outside to inside: Escherichia coli K12 COG categories (two circles), genes identified by SIGI (two circles), genes listed in the Horizontal Gene Transfer Database [18] (two circles), standard deviations of genes identified by IslandPath (single circle, red +ve, green -ve), mean centered GC content of the genome (red: above mean, blue: below mean), GC content of the genome again as a single-sided line plot (green).

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