Computational tools and Interoperability in Comparative ... - CBS

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rRNA operons and promoter analysis
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A T T G G T Y A A A W T T T R A C C A A T
Figure 3.4: Logo plots showing the initial weight matrices used for searching E. coli and Shigella
genomes: –10 hexamer (a), –35 hexamer (b), UP element (c), and FIS binding motif (d).
The 16S rRNA genes of all E. coli and Shigella genomes were annotated using RNAmmer.
For the list of genomes, see table 3.1. All 16S rRNA genes were aligned using clustalw
(Thompson et al., 1994) and a neighbor-joining tree was constructed (see figure 3.5). The
figure shows additional Salmonella and Yersinia genomes for comparison.
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