restriction enzymes in dna fingerprinting

[mattw]

In DNA comparisons between two people, which genes or sequences are chosen to compare? You can't compare all the chromosomes, because there are 3 billion base pairs. So which restriction enzymes are used, which sections of dna are chosen for comparison, how are they selected out, and how are the genes that are not going to be compared thrown away?
Many thanks,
Matt

[canalon]

In a few year if sequencing cost keep going down, it will be possible to compare all genomes indeed. The 1000 dollars genome has never been so close.

But in the mean time there are quite a few different techniques that are used, and they are quickly and accurately presented in the pit of all evil: http://en.wikipedia.org/wiki/DNA_profiling