Computational tools and Interoperability in Comparative ... - CBS

Fig. 6 Genomic properties of Streptomyces coelicolor A3. a Comparison
of AT content upstream and downstream of all 7,825 genes; the
genes are all oriented in the same direction and aligned such that the
translation start site is in the middle. Z-scores of standard deviations
from the chromosomal average are plotted, as described previously
(Ussery and Hallin 2004a). b Codon usage of the same set of 7825
genes. The frequency of occurrence of each of the 64 codons is plotted
in a star plot; note that most codons have a relatively low frequency of
usage. c Bias in the codon position are plotted as frequencies; note that
seen for many other bacterial genomes. For example, in
Fig. 7b, there are four large gaps in the C. jejuni RM1221
genome compared to other epsilon Proteobacteria. These
correspond to phage insertion sites in C. jejuni RM1221, as
described in the original genome sequence publication
(Fouts et al. 2005). Similar results have been observed for
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there is a strong tendancy for Cs and Gs in third position. d Amino acid
usage of each of the 20 amino acids for the entire S. coelicolor
proteome is plotted as frequency of the total; the amino acids in this plot
are grouped according to their properties; for example, all the aliphatic
amino acids (A, V, L, I and G) are together and, in general, there is a
general trend for this proteome to favour aliphatic amino acids, with the
exception of isoleucine. The three star plots are as described previously
(Ussery et al. 2004c)
Streptococcus (Hallin et al. 2004a). In all three of these
cases, there are large regions which contain many genes
which are missing in other genomes of the same species.
These clusters of genes often contain evidence that they
came from phages, which appears to be an efficient method
of bringing new DNA into a genome.