Protein proteolytic enzyme or reagent cleavage digest emboss digest -seqall $input1 -outfile $out_file1 -menu $menu -unfavoured $unfavoured -overlap $overlap -allpartials $allpartials -rformat2 $out_format1 -auto Sequence Enzyme/Reagent Trypsin Lys-C Arg-C Asp-N V8-bicarb V8-phosph Chymotrypsin CNBr Trypsin will not normally cut after a K if it is followed by (e.g.) another K or a P. Specifying this shows those cuts, as well as the favoured ones. No Yes Used for partial digestion. Shows all cuts from favoured cut sites plus 1..3, 2..4, 3..5 etc but not (e.g.) 2..5. Overlaps are therefore fragments with exactly one potential cut site within it. No Yes As for overlap but fragments containing more than one potential cut site are included. No Yes Output Report File Format SeqTable EMBL GENBANK GFF PIR SwissProt DbMotif Diffseq Excel (tab delimited) FeatTable Motif Regions SRS Simple SRS Table TagSeq You can view the original documentation here_. .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/digest.html