Below is an example of how to use nip to search for the restriction cloning site.
Select operation
X 1 Search
2 List enzyme file
3 Clear text
4 Clear graphics
? Selection (1-4) (1) =
Select input source
1 All enzymes file
X 2 Six cutter file
3 Four cutter file
4 Personal file
5 Keyboard
? Selection (1-5) (2) =
? Search for all names (y/n) (y) = n
? Name=smai
? Name=
Select results display mode
X 1 Order results enzyme by enzyme
2 Order results by position
3 Show only infrequent cutters
4 Show names above the sequence
? Selection (1-4) (1) =
? List matches (y/n) (y) =
? The sequence is circular (y/n) (y) =
? Search for definite matches (y/n) (y) =
Working
Matches found= 1
Name Sequence Position Fragment lengths
1 SMAI ccc'ggg 6249 7249 7249
Searching for the SmaI site (6249) in M13MP18.