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.