]> Protein proteolytic enzyme or reagent cleavage digest (EMBOSS) protein:motifs http://bioweb.pasteur.fr/docs/EMBOSS/digest.html digest &emboss_init; input Input section sequence sequence -- Protein [single sequence] (-sequence) perl " -sequence=$value -sformat=fasta" 1 protein 8 seqfile perl 1 required Required section menu Select number -- Enzymes and Reagents (-menu) 1 Trypsin 2 Lys-C 3 Arg-C 4 Asp-N 5 V8-bicarb 6 V8-phosph 7 Chymotrypsin 8 CNBr 1 perl " -menu=$value" 2 advanced Advanced section unfavoured Allow unfavoured cuts (-unfavoured) perl ($value)? " -unfavoured" : "" 3 Trypsin will not normally cut after a K if it is followed by (e.g.) another K or a P. Specifying this shows those cuts. as well as the favoured ones. aadata Amino acid data file (-aadata) Eamino.dat perl ($value && $value ne $vdef)? " -aadata=$value" : "" 4 Molecular weight data for amino acids output Output section overlap Show overlapping partials (-overlap) perl ($value)? " -overlap" : "" 5 Used for partial digestion. Shows all cuts from favoured cut sites plus 1..3, 2..4, 3..5 etc but not (e.g.) 2..5. Overlaps are therefore fragments with exactly one potential cut site within it. allpartials Show all partials (-allpartials) perl ($value)? " -allpartials" : "" 6 As for overlap but fragments containing more than one potential cut site are included. outfile outfile (-outfile) outfile.out perl " -outfile=$value" 7 auto perl " -auto -stdout" 9