Computational tools and Interoperability in Comparative ... - CBS

Comparative Genomics
1 mysql -N -B -D genomeatlas3_cur -e " select p.grp , concat (’#’, color )
,ord , sum ( length ),concat ( organism_name ,’/’, segment_name ,’/’,
genbank ) from atlasdb as a, genbank_complete_prj as p ,
genbank_complete_seq as s , phyla as ph where s. genbank = a.
accession and s. pid = p. pid and segment_name not like ’genome %’
and ph. phyla = p. grp group by s. pid " > length . tbl
2 set N = ‘wc -l < length .tbl ‘
3 ~ pfh / scripts / boxplot -main " Size distribution of Prokaryotic
genomes (N = $N)" < length . tbl > length .ps
4 mysql -N -B -D genomeatlas3_cur -e " select p.grp , concat (’#’, color )
,ord , sum ( atcontent * length )/ sum ( length ),concat ( organism_name
,’/’, segment_name ,’/’, genbank ) from atlasdb as a,
genbank_complete_prj as p , genbank_complete_seq as s , phyla
as ph where s. genbank = a. accession and s. pid = p. pid and
segment_name not like ’genome %’ and ph. phyla = p. grp group by s
. pid "> atcontent . tbl
5 ~ pfh / scripts / boxplot -main "AT content distribution of Prokaryotic
genomes (N = $N)" < atcontent . tbl > atcontent .ps
The tables generated by the MySQL query can be read by the boxplot program, which
is a Perl wrapper for the R command boxplot, and a PostScript document is generated.
Figure 2.4 shows the total genome length (including all replicons) of all published prokaryotic
genomes, divided into phyla. The confidence interval appears wide for many groups,
reflecting a high intra-phyla variation. However, for a number of phyla the difference
is significant. The β-protebacteria tend to have longer chromosomes than for example
the firmicutes, the α-proteobacteria, and the cyanobacteria. It is also evident that the
δ-proteobacteria Sorangium cellulosum Soce56 represents the longest genome (13,033,779
nt, Schneiker et al. (2007)) but that this is an outlier not representative of the entire phylum.
The shortest bacterial genome published so far is the α-proteobacterium Candidatus
Hodgkinia cicadicola Dsem (143,795 nt, McCutcheon et al. (2009)). Thus, the difference
between the smallest and the largest is close to 100 fold. The plot in figure 2.3 shows the
fraction of AT for the prokaryotic genomes ranging from 25% for the δ-proteobacterium
Anaeromyxobacter dehalogenans 2CP-C (Sanford et al., 2002) to 83% for Candidatus Carsonella
ruddii PV (Nakabachi et al. (2006).
2.3.2 heatmap - 2D clustering
A way to increase the dimensionality for visualizing genomic properties is by using a socalled
heatmap or 2D clustering. Instead of looking at a single property at a time (e.g.
length or AT content), multiple features may be included in the same plot. The axis is
replaced with a color transformation of the data and different normalization methods may
be applied. In the example below a comparison is made for 87 Enterobacteriaceae, covering
among others the genera of Escherichia, Salmonella, Yersinia, Shigella, Buchnera, and
Klebsiella. The CBS Genome Atlas Database is queried for the features such as tRNA and
rRNA gene count, total coding genes, genome size, AT content, simple genomic repeats,
local direct repeats, base pairs per gene, and coding fraction of the genome. The plot
is shown in figure 2.5 and the R code for producing the plot is shown below in listing
2.8. The data have been normalized to allow for comparison. Features and organisms are
hierarchically clustered to group organisms with similar properties and to gorup properties
that correlate within the organisms.
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