Finding of origin of replication in a bacterial Genome

Question

[Optimist]

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

Answer 1

[harold.smith.tarheel]

Computationally? There's Ori-Finder.

Answer 2

[Brian Bushnell]

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.