Virtual Electrophoresis - (Sep/18/2012 )
For people who never did this in reality (or who want to check a plasmid digest virtually):
I use the freeware ape/>ApE (A Plasmid Editor) that has this built in as one of the functions. It's pretty cool - you can mouse over the fragments and it will tell you the size, which enzymes it was cut with, the positions and the relative mass percent.
NEB cutter has virtual electrophoresis as one of its tools. And doesn't require Java.