DNA replication Finding origin of replication in bacteria

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DNA replicationFinding origin of replication in
bacteria

• Peder Worning
• Center for Biological Sequence Analysis

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DNA Replication
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Leading and lagging strands
Leading strand is made continuously
Lagging strand is made discontinuously
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Bidirectionel DNA-Replication
of a Circular Genome
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DNA Replication in Bacteria and Eukaryotes
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Photos of DNA Replication
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Origin and Terminus, Leading and Lagging Strands
Looking for borders between the leading and the
lagging strands. Using the difference in the
composition of the leading and the
lagging Strands. Counting frequencies of oligo
nucleotides
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Strand Difference
We measure the difference between the leading and
the lagging strand by counting all
oligonucleotides up to 8mers and compare the
number each oligo appears in the two strands. We
then calculate the information content of this
difference for every oligo, i.
Ii ( Ni,lead - Ni,lagg )log2((Ni,lead R)/(
Ni,lagg R))
The information content is summed over all oligos
for every putative origin position, p.
I(p) ? Ii(p)
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The strand difference curve
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Bacillus subtilisWindow size 60
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Origin versus Terminus the G/C skew
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The Window size I
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The Window size II
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The Median of five window sizes
Thermotoga maritima
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The signal to noise ratio
Signal strength
IC I(p,max) - I(p,min)
Signal to noise ratio
S/N IC / I(p,min)
Clostridium perifrigens 43.79
Bacillus subtilis 11.10
Echerichia coli 2.30
Thermotoga maritima 0.80
Synechocystis 0.12
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Two Bacillus genomes
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A dot plot
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Two Pseudomonas genomes
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Another dot plot
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Archaeal Genomes
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Halobacterium an extreme halophilic archaea