PEPDIGEST(1e) | EMBOSS Manual for Debian | PEPDIGEST(1e) |
NAME¶
pepdigest - Reports on protein proteolytic enzyme or reagent cleavage sitesSYNOPSIS¶
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 datafileMolecular weight data for amino acids Default value:
Emolwt.dat
Required section¶
-menu listDefault value: 1
-mono boolean
Default value: N
Advanced section¶
-unfavoured booleanTrypsin 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 booleanUsed 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.05/11/2012 | EMBOSS 6.4.0 |