Figure 1.

BRIG output image of a simulated draft E. coli O157:H7 str. Sakai genome. Figure 1 shows a draft E. coli genome compared against 27 other prokaryote genomes (the full list of genomes is described in Table 1). The reference genome is an ordered set of contigs, assembled using GS De Novo Assembler (454 Life Sciences/Roche) version 2.3, from simulated sequencing reads generated by MetaSim [21] based on the E. coli O157:H7 str. Sakai genome [GenBank:BA000007]. After assembly contigs were ordered against the complete E. coli O157:H7 Sakai genome using Mauve [7]. The innermost rings show GC skew (purple/green) and GC content (black). The third innermost ring shows genome coverage (brown); genome regions with coverage more than one standard deviation (~ 41) from the mean coverage (~ 94) are represented as blue spikes. Contig boundaries are shown outside this ring as alternating red and blue bars. The remaining rings show BLAST comparisons of 27 other complete E. coli and Salmonella genomes against the simulated draft genome assembly (in several cases, multiple genome comparisons are collapsed into a single ring, Table 1). The outermost ring highlights the Sakai prophage, and prophage-like (Sp & SpLE) regions as described by Hayashi et al. [20], shown in navy blue and fuchsia, respectively. SpLE 4, containing the locus of enterocyte effacement, is shown in green.

Alikhan et al. BMC Genomics 2011 12:402   doi:10.1186/1471-2164-12-402
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