Finding of origin of replication in a bacterial Genome
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4.8 years ago
Optimist ▴ 180

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

Bacterial genomics Bioinformatics NGS WGS oriT • 1.9k views
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Entering edit mode
4.8 years ago

Computationally? There's Ori-Finder.

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Entering edit mode
4.8 years ago

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.