digest1e
Reports on protein proteolytic enzyme or reagent cleavage sites
Usage
digest -seqall
seqall
-mwdata
datafile
-menu
list
-mono
boolean
-unfavoured
boolean
-ragging
boolean
-termini
list
-overlap
boolean
-allpartials
boolean
-outfile
report
digest -help
Overview
digest is a command line program from EMBOSS (“the European Molecular Biology Open Software Suite”). It is part of the "Protein:Motifs" command group(s).
Options
Input section
-
-seqall seqall
-
-mwdata datafile -
Molecular weight data for amino acids Default value: Emolwt.dat
Required section
-
-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
Releases
9 releases since Debian 5.0 (Lenny); the text changed 2 times.
-mono since Debian 6.0 (Squeeze);
-mwdata since Debian 6.0 (Squeeze).
-aadata until Debian 5.0 (Lenny).