NAME

       pepdigest - Reports on protein proteolytic enzyme or reagent cleavage sites

SYNOPSIS

       pepdigest -seqall seqall -mwdata datafile -menu list -mono boolean -unfavoured boolean -ragging boolean
                 -termini list -overlap boolean -allpartials boolean -outfile report

       pepdigest -help

DESCRIPTION

       pepdigest is a command line program from EMBOSS (“the European Molecular Biology Open Software Suite”).
       It is part of the "Protein:Composition" command group(s).

OPTIONS

   Input section
       -seqall seqall

       -mwdata datafile
           Molecular weight data for amino acids Default value: Emolwt.dat

   Required section
       -menu list
           Default value: 1

       -mono boolean
           Default value: N

   Advanced section
       -unfavoured boolean
           Trypsin will not normally cut after 'KR' if they are followed by any of 'KRIFLP'. Lys-C will not
           normally cut after 'K' if it is followed by 'P'. Arg-C will not normally cut after 'R' if it is
           followed by 'P'. V8-bicarb will not normally cut after 'E' if it is followed by any of 'KREP'.
           V8-phosph will not normally cut after 'DE' if they are followed by 'P'. Chymotrypsin will not
           normally cut after 'FYWLM' if they are followed by 'P'. Specifying unfavoured shows these unfavoured
           cuts as well as the favoured ones.

       -ragging boolean
           Allows semi-specific and non-specific digestion. This option is particularly useful for generating
           lists of peptide sequences for protein identification using mass-spectrometry.

       -termini list
           Default value: 1

   Output section
       -overlap boolean
           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 boolean
           As for overlap but fragments containing more than one potential cut site are included.

       -outfile report

BUGS

       Bugs can be reported to the Debian Bug Tracking system (http://bugs.debian.org/emboss), or directly to
       the EMBOSS developers (http://sourceforge.net/tracker/?group_id=93650&atid=605031).

SEE ALSO

       pepdigest is fully documented via the tfm(1) system.

AUTHOR

       Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
           Wrote the script used to autogenerate this manual page.

COPYRIGHT

       This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package. It can be
       redistributed under the same terms as EMBOSS itself.

EMBOSS 6.4.0                                       05/11/2012                                      PEPDIGEST(1e)