Certain regions of the genome are known to be different across species. These regions come in handy when trying to identify species, or even individuals. To work with these regions, DNA is extracted from the organism (a few cells are enough) and then these regions are amplified. The amplification step is done using polymerase chain reaction (PCR).

To cut DNA at specific locations restriction enzymes are used. These are enzymes first found in bacteria. The first one ever found was called EcoRI. This is a protein which associates with DNA. It does this most preferably at the nucleotide acid sequence GAATTC. Once it reaches such a sequences it digests it in a way that creates a cut between G and A: G/AATTC.

This reaction is performed with the amplified regions of the extracted DNA. It will create DNA fragments of differing length. The combination of fragment sizes is very specific to each species.

To actually see these fragments a gel electrophoresis is performed. In short, the DNA fragments are forced to move through a gel by voltage. This works because DNA is negatively charged. The gel acts as a barrier which slows down the DNA fragments. Shorter fragments can move faster through this barrier than longer ones. Therefore, DNA fragments start to separate by length.

Sequences from the Ribulose-bisphosphate carboxylase and Maturase K genes of plants were digested with EcoRI in silico.