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     Output report file name

   Optional qualifiers: (none)
   Advanced qualifiers:
   -unfavoured         boolean    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            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.

   General qualifiers:
  -help                boolean    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)
Output report file name 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      TPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIER
    178     231 6335.495   R      E      YIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVK
     22      69 5788.873   R      T      SPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLR
    253     296 5004.085   R      S      MVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAK
    136     177 4600.460   R      Y      YVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSR
      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:

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 nameDescription
antigenicFinds antigenic sites in proteins
fuzzproProtein pattern search
fuzztranProtein pattern search after translation
helixturnhelixReport nucleic acid binding motifs
oddcompFinds protein sequence regions with a biased composition
patmatdbSearch a protein sequence with a motif
patmatmotifsSearch a PROSITE motif database with a protein sequence
pepcoilPredicts coiled coil regions
pregRegular expression search of a protein sequence
pscanScans proteins using PRINTS
sigcleaveReports 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