Finding of origin of replication in a bacterial Genome
Hello all,
How do I detect the presence of Origin of replication in my bacterial genome.
Are there any tools for this purpose?
Thanking you all
Optimist
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2 answers
Computationally? There's Ori-Finder.
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If you have WGS sequence from an isolate that was in growth phase (which they often are), you can map it to the genome and calculate coverage, e.g.
bbmap.sh in=reads.fq ref=bacteria.fa bincov=binned_coverage.txt
Then if you plot the coverage in R/Excel, the coverage will typically vary by about 2-fold from the origin of replication (highest) to the antipode (lowest), forming a triangular distribution. That can narrow down the origin to maybe... a 50kbp range? I'm not sure how well Ori-Finder works, but this could be used to validate its answer.
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