Analyze: Restriction Enzyme Sites in R.T. Proteins
Analyze: Restriction Enzyme Sites in Reverse Translated Proteins window looks almost exactly the same as in the option Restriction Enzyme Sites, with the same features displayed. The bottom window shows the search range and the type of enzyme cuts that have been considered: blunt ends, 3’ or 5’-overhangs or other (odd).
This search can be performed only on the positive strand sequence in any of the 3 reading frames. It is helpful to use Open Reading Frames window, select the ORF of interest from there and read the exact search range that needs to be performed.
This is the analysis of a protein, so the actual nucleotide sequence has little to do with it. The sites in the potential DNA sequence are calculated only from reverse translated protein using the degenerate method, and the window displays all possible restriction sites that could be used in the DNA sequence without changing the protein sequence. Example of the window is shown above.
OLIGO has 79 restriction enzymes that can be selected for the search. All are six-base cutters or longer, and none recognize degenerate bases.