Computational tools and Interoperability in Comparative ... - CBS

Genome Comparisons
Right whisker ends at an observed
data point, not exceeding 1.5 IQR
1.5 x IQR
95% confidence interval
Q1 IQR Q3
1.5 x IQR
median
Right whisker ends at an observed
data point, not exceeding 1.5 IQR
Mild outliers between 1.5 and 3.0 IQR
and extreme outliers more than 3 IQR
away from Q1 and Q3
Figure 2.2: Construction of a box-and-whiskers plot. Notches is an estimate of the 95% confidence
interval.
The tools presented here have all been used widely during course activities and research
projects.
2.3.1 Box-and-wiskers plot
As the number of sequenced bacterial genomes grew from only two in 1995 to now close to a
thousand at the time of writing, there began to be enough data to sample various genomic
properties amongst the different phylogenetic groups. The box-and-wiskers plot (Tukey,
1977) is a useful tool for visualizing such differences. The plot shows a box between the
first and the third quantile (figure 2.2). The distance between Q1 and Q3 is called the Inter
Quantile Ratio (IQR) and whiskers are drawn through observations that are not exceeding
1.5 × IQR. A line is drawn within the box representing the median. Data between
1.5 × IQR and 3.0 × IQR are denoted ”mild” outliers whereas observations exceeding
3.0 × IQR are extreme outliers. Notches are sometimes drawn to denote the confidence
interval. In the R implementation of the box-and-wiskers plot the 95% confidence interval
is approximated by 1.5×IQR
√ . When comparing two or more distributions, non-overlapping
N
notches marks significant differences.
Distribution of genome size and base composition in prokaryotes
To examine the base composition and genome size for different phylogenetic groups, a
query to the CBS Genome Atlas Database can be done, grouping replicons into projects
and summarizing / averaging within each project. Altough only possible from within CBS,
the commands are listed below.
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