Search: for Restriction Enzyme Sites
The search for restriction enzymes window has a simple interface, shown above. The restriction enzyme database is in a NEB- type 2 format. Oligo provides six databases, and the most useful is "NICE6&UP", that contains mostly used commercial enzymes recognizing 6 or more base pairs. The results are displayed in the Analyze window. You may also search for transcription factor sites by replacing a *.enz file for "transcription factors.txt", already provided. You may create your own text file that could serve as the search template (if you'd give it an .enz extension Oligo would open it automatically).
Oligo can search for restriction sites in reverse translated proteins. The interface is similar to the standard search in DNA sequence files. The results are displayed in one of the Analyze menu options.