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.