Question: Finding of origin of replication in a bacterial Genome
0
gravatar for Optimist
3.3 years ago by
Optimist100
Optimist100 wrote:

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

ADD COMMENTlink modified 3.3 years ago by Brian Bushnell17k • written 3.3 years ago by Optimist100
2
gravatar for harold.smith.tarheel
3.3 years ago by
United States
harold.smith.tarheel4.6k wrote:

Computationally? There's Ori-Finder.

ADD COMMENTlink written 3.3 years ago by harold.smith.tarheel4.6k
0
gravatar for Brian Bushnell
3.3 years ago by
Walnut Creek, USA
Brian Bushnell17k wrote:

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.

ADD COMMENTlink written 3.3 years ago by Brian Bushnell17k
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