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progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement

Figure 9

A Mauve visualization of the hypervariable intergenic regions surrounding yhdE.

Each genome is laid out in a horizontal track, with annotated coding regions shown as white boxes. A colored similarity plot is shown for each genome, the height of which is proportional to the level of sequence identity in that region. When the similarity plot points downward it indicates an alignment to the reverse strand of the genome. Colors in the similarity plot indicate the combination of organisms containing a particular segment of the genome. Segments colored pink/mauve are conserved among all organisms, while purple segments are conserved in everything but Salmonella, and segments colored in olive green are conserved among non-uropathogenic E. coli. The visualization system is interactive and written in Java, and works on all computers supporting Java 1.4 or later.

Figure 9

doi: https://doi.org/10.1371/journal.pone.0011147.g009