
                               EMBOSS: digest
     _________________________________________________________________
   
                                Program digest
                                       
Function

   Protein proteolytic enzyme or reagent cleavage digest
   
Description

   digest finds the positions where a specified proteolytic enzyme or
   reagent might cut a peptide sequence.
   
   This programs allows you to input a protein sequence and to specify
   one proteolytic agent from a list. It will then output a file
   containing the positions where the agent cuts, together with the
   peptides produced.
   
   Trypsin will not normally cut after a K if it is followed by (e.g.)
   another K or a P. Specifying the qualifier -unfavoured shows those
   cuts. as well as the favoured ones.
   
   If you wish to emulate a partial digestion, then using the -overlap
   qualifier will display the results from a digest in which all cut
   sites are used and in which one site at a time is not cut. Thus the
   resulting peptide fragments from the cut sites numbered 1, 2, 3, 4
   etc. are shown, plus the fragments produced by cutting at the sites
   1..3, 2..4, etc.
   
   i.e. fragments containing one potential cut site are also shown.
   
   If you wish to emulate a very partial digestion (!) then using the
   -allpartials qualifier will do what -overlap did, but also show all
   possible fragments from using all possible combinations of cut sites.
   For example, fragments from the cut sites numbered 1, 2, 3, 4, 5 and
   from the fragments produced by cutting between sites 1..3, 1..4, 1..5,
   2..4, 2..5, 3..5, etc.
   
   i.e. fragments containing one or more potential cut site are also
   shown.
   
Usage

   Here is a sample session with digest.

% digest
Input sequence: sw:opsd_human
Enzymes and Reagents
         1 : Trypsin
         2 : Lys-C
         3 : Arg-C
         4 : Asp-N
         5 : V8-bicarb
         6 : V8-phosph
         7 : Chymotrypsin
         8 : CNBr
Select number [1]:
Output file [opsd_human.digest]:

Command line arguments

   Mandatory qualifiers:
  [-sequencea]         sequence   Sequence USA
   -menu               menu       Select number
  [-outfile]           report     (no help text) report value

   Optional qualifiers: (none)
   Advanced qualifiers:
   -unfavoured         bool       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             string     Molecular weight data for amino acids
   -overlap            bool       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        bool       As for overlap but fragments containing more
                                  than one potential cut site are included.

   General qualifiers:
  -help                bool       report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   

   Mandatory qualifiers Allowed values Default
   [-sequencea]
   (Parameter 1) Sequence USA Readable sequence Required
   -menu Select number
   1 (Trypsin)
   2 (Lys-C)
   3 (Arg-C)
   4 (Asp-N)
   5 (V8-bicarb)
   6 (V8-phosph)
   7 (Chymotrypsin)
   8 (CNBr)
   1
   [-outfile]
   (Parameter 2) (no help text) report value Report file
   Optional qualifiers Allowed values Default
   (none)
   Advanced qualifiers Allowed values Default
   -unfavoured 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. Yes/No No
   -aadata Molecular weight data for amino acids Any string is accepted
   Eamino.dat
   -overlap 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.
   Yes/No No
   -allpartials As for overlap but fragments containing more than one
   potential cut site are included. Yes/No No
   
Input file format

   Any protein sequence.
   
Output file format

   The output is a standard EMBOSS report file.
   
   The results can be output in one of several styles by using the
   command-line qualifier -rformat xxx, where 'xxx' is replaced by the
   name of the required format. The available format names are: embl,
   genbank, gff, pir, swiss, trace, listfile, dbmotif, diffseq, excel,
   feattable, motif, regions, seqtable, simple, srs, table, tagseq
   
   See:
   http://www.uk.embnet.org/Software/EMBOSS/Themes/ReportFormats.html for
   further information on report formats.
   
   By default digest writes a 'seqtable' report file.
     _________________________________________________________________
   
########################################
# Program: digest
# Rundate: Mon Feb 11 13:36:16 2002
# Report_file: opsd_human.digest
########################################

#=======================================
#
# Sequence: OPSD_HUMAN     from: 1   to: 348
# HitCount: 14
#
# Complete digestion with Trypsin yields 14 fragments
#
#=======================================

  Start     End Mol_Weight cterm  nterm  Sequence
     70     135 7129.319   R      Y      TPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGP
TGCNLEGFFATLGGEIALWSLVVLAIER
    178     231 6335.495   R      E      YIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIP
MIIIFFCYGQLVFTVK
     22      69 5788.873   R      T      SPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTL
YVTVQHKKLR
    253     296 5004.085   R      S      MVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTI
PAFFAK
    136     177 4600.460   R      Y      YVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLA
GWSR
      1      21 2257.495   .      S      MNGTEGPNFYVPFSNATGVVR
    297     311 1728.089   K      Q      SAAIYNPVIYIMMNK
    232     245 1490.538   K      A      EAAAQQQESATTQK
    326     339 1403.457   K      T      NPLGDDEASATVSK
    315     325 1186.476   R      N      NCMLTTICCGK
    340     348 902.950    K      .      TETSQVAPA
    249     252 503.550    K      M      EVTR
    312     314 449.504    K      N      QFR
    246     248 346.378    K      E      AEK

#---------------------------------------
#---------------------------------------
     _________________________________________________________________
   
   The header information contains the propgram name, date of run, name
   of the reagent used to digest the protein and the number of fragments
   reported. The header will report if complete or partial digestion was
   chosen.
   
   The rest of the file consists of columns holding the following data:
     * The start position of the fragment
     * The end position of the fragment
     * The molecular weight of the fragment
     * The residue before the cut site ('.' if start of sequence)
     * The residue after the second cut site ('.' if end of sequence)
     * The sequence of the fragment.
       
Data files

   None.
   
Notes

   None.
   
References

   None.
   
Warnings

   None.
   
Diagnostic Error Messages

   None.
   
Exit status

   ALways exist with a status of 0.
   
Known bugs

   None.
   
See also

    Program name                        Description
   antigenic      Finds antigenic sites in proteins
   fuzzpro        Protein pattern search
   fuzztran       Protein pattern search after translation
   helixturnhelix Report nucleic acid binding motifs
   oddcomp        Finds protein sequence regions with a biased composition
   patmatdb       Search a protein sequence with a motif
   patmatmotifs   Search a PROSITE motif database with a protein sequence
   pepcoil        Predicts coiled coil regions
   preg           Regular expression search of a protein sequence
   pscan          Scans proteins using PRINTS
   sigcleave      Reports protein signal cleavage sites
   
Author(s)

   This application was written by Alan Bleasby (ableasby@hgmp.mrc.ac.uk)
   
History

   Written (1999) - Alan Bleasby
   
Target users

   This program is intended to be used by everyone and everything, from
   naive users to embedded scripts.
   
Comments
