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eplication tends to be more GC rich, and the region around the replication terminus usually
is more ATrich. AT-rich sequences melt more easily than GC-rich sequences, due in part to the
extra hydrogen bond present in a GC base pair. Contra-intuitively, this would make the origin
of replication the least likely to start replication. However, within the ‘‘large region’’ around
the origin of approximately 5% of the chromosome, there is a short stretch of more AT rich
basepairs, where the replication origin bubble opens up. Second, and zooming in at genes, the
average GC content of intergenic regions is generally lower than that of coding sequences.
These regions will melt more readily, are more curved and more rigid than the chromosomal
average, in order to enable gene expression (Pedersen et al., 2000, Ussery and Hallin, 2004).
This is true for nearly all of the bacterial genomes sequenced, regardless of GC content. In order
to calculate relative or local %GC, a window has to be defined (say, investigating 100 basepairs)
for which the %GC is calculated. This window is then moved along the genome by singlenucleotide
steps, and the %GC is scored related to the middle of each window. These scores can
then be graphically represented. A web-based tool for this is available at the Genome Atlas
Website 2 in which local %GC can be visualized by color codes as discussed below.
3 Visualization of Genomic Data: The Genome Atlas
Genome atlases are circular plots of chromosomes or plasmids (a linear version is available
when applicable) on which general properties of the DNA molecule are plotted as colors.
Genome atlases are available from our web server 2 for many of the currently sequenced
bacterial genomes. > Figure 2 shows a Genome Atlas for the chromosome of Geobacillus
kaustophilus strain HTA426 (a thermophilic Firmicute that also contains a plasmid of 4.8 kb).
This isolate was obtained from a deep sea sediment of the Mariana Trench in the Pacific Ocean
(Takami et al., 2004a, b). Its genome is 3.5 Mbp long and contains 52.1% GC. G. kaustophilus
has been suggested to provide a possible solution for paraffin deposition problems with oil
production (Sood and Lal, 2008). A Genome Atlas maps four different aspects of the
chromosomal DNA sequence in various lanes in a standard manner: DNA structural features
are represented in the three outer lanes, all coding sequences are indicated in the next lane, two
kinds of repeats are mapped in the next two lanes, and base composition properties are plotted
in the two innermost lanes (Jensen et al., 1999). The scale in the center corresponds with the
sequence numbering in GenBank. The DNA structural features of the three outermost circles
are based on the physical chemical properties of the DNA helix. The annotated genes are given
in blue for protein-coding genes oriented clockwise, and red for genes on the other strand
(counterclockwise). The tRNA and rRNA genes have their own color. The clockwise strand
corresponds with the sequence stored in GenBank (genes on the other strand are annotated as
‘‘complement’’ in there). To identify global repeats (sequences that are repeated somewhere
else on the chromosome) we search for the best match of a 100 bp window against the entire
chromosome. Searching on the positive strand results in direct repeats (both sequences run in
the same direction) whilst searching on the negative strand gives inverted repeats (the two
repeat units run in opposite directions). For most of these general properties summarized in a
Genome Atlas (structural properties, repeats, base composition) dedicated atlases are also
available, where more features are given (such as local and simple repeats in a Repeat Atlas, or
2 http://www.cbs.dtu.dk/services/GenomeAtlas/
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