digest finds the positions where a specified proteolytic enzyme or reagent might cut a peptide sequence.

Here is a sample session with digest:

% digest
Input sequence: sw:opsd_human
Enzymes and Reagents
         1 : Trypsin
         2 : Lys-C
         3 : Arg-C
         4 : Asp-N
         5 : V8-bicarb
         6 : V8-phosph
         7 : Chymotrypsin
         8 : CNBr
Select number [1]:
Output file [opsd_human.digest]:

Mandatory qualifiers:

[-sequencea] (sequence)

Sequence USA.

-menu (menu)

Select number.

[-outfile] (report)

Output report filename.

Advanced qualifiers:

-unfavoured (boolean)

Trypsin will not normally cut after a K if it is followed by another K or a P. Specifying this shows those cuts as well as the favoured ones.

-aadata (string)

Molecular weight data for amino acids.

-overlap (boolean)

Used for partial digestion. Shows all cuts from favoured cut sites plus 1-3, 2-4, 3-5, etc. Overlaps are fragments with exactly one potential cut site within them (e.g., 2-5 is invalid).

-allpartials (boolean)

Similar to overlap, but fragments containing more than one potential cut site are included.