Rather than relying solely on restriction enzyme digestion, include the ability to simulate free shearing of DNA at any point.
This can be a simulation of
dnase digestion
mechanical shearing.
In the first case, there are already publications demonstrating the method, in the second, it would appear we have evidence of randomly sheared sites participating in ligation products. This was likely the outcome of damage during lysis of more easily popped cells.
Rather than relying solely on restriction enzyme digestion, include the ability to simulate free shearing of DNA at any point.
This can be a simulation of
In the first case, there are already publications demonstrating the method, in the second, it would appear we have evidence of randomly sheared sites participating in ligation products. This was likely the outcome of damage during lysis of more easily popped cells.