                                  pepdigest



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Function

   Report on protein proteolytic enzyme or reagent cleavage sites

Description

   This programs allows you to input one or more protein sequences and to
   specify one proteolytic agent from a list, which might be a proteolytic
   enzyme or other reagent. It will then write a report file containing
   the positions where the agent cuts, together with the peptides
   produced.

Algorithm

   By default pepdigest uses average molecular weights. The -mono option
   will use monoisotopic weights.

Usage

   Here is a sample session with pepdigest


% pepdigest
Report on protein proteolytic enzyme or reagent cleavage sites
Input protein sequence(s): tsw: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]:
Use monoisotopic weights [N]:
Output report [opsd_human.pepdigest]:


   Go to the input files for this example
   Go to the output files for this example

Command line arguments

Report on protein proteolytic enzyme or reagent cleavage sites
Version: EMBOSS:6.5.6.0

   Standard (Mandatory) qualifiers:
  [-seqall]            seqall     Protein sequence(s) filename and optional
                                  format, or reference (input USA)
   -menu               menu       [1] Select number (Values: 1 (Trypsin); 2
                                  (Lys-C); 3 (Arg-C); 4 (Asp-N); 5
                                  (V8-bicarb); 6 (V8-phosph); 7
                                  (Chymotrypsin); 8 (CNBr))
   -mono               boolean    [N] Use monoisotopic weights
  [-outfile]           report     [*.pepdigest] Output report file name
                                  (default -rformat seqtable)

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -mwdata             datafile   [Emolwt.dat] Molecular weight data for amino
                                  acids
   -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            menu       [1] Select number (Values: 1 (none); 2
                                  (nterm); 3 (cterm); 4 (nterm OR cterm))
   -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.

   Associated qualifiers:

   "-seqall" associated qualifiers
   -sbegin1            integer    Start of each sequence to be used
   -send1              integer    End of each sequence to be used
   -sreverse1          boolean    Reverse (if DNA)
   -sask1              boolean    Ask for begin/end/reverse
   -snucleotide1       boolean    Sequence is nucleotide
   -sprotein1          boolean    Sequence is protein
   -slower1            boolean    Make lower case
   -supper1            boolean    Make upper case
   -scircular1         boolean    Sequence is circular
   -sformat1           string     Input sequence format
   -iquery1            string     Input query fields or ID list
   -ioffset1           integer    Input start position offset
   -sdbname1           string     Database name
   -sid1               string     Entryname
   -ufo1               string     UFO features
   -fformat1           string     Features format
   -fopenfile1         string     Features file name

   "-outfile" associated qualifiers
   -rformat2           string     Report format
   -rname2             string     Base file name
   -rextension2        string     File name extension
   -rdirectory2        string     Output directory
   -raccshow2          boolean    Show accession number in the report
   -rdesshow2          boolean    Show description in the report
   -rscoreshow2        boolean    Show the score in the report
   -rstrandshow2       boolean    Show the nucleotide strand in the report
   -rusashow2          boolean    Show the full USA in the report
   -rmaxall2           integer    Maximum total hits to report
   -rmaxseq2           integer    Maximum hits to report for one sequence

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options and exit. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report dying program messages
   -version            boolean    Report version number and exit


Input file format

   Any protein sequence.

  Input files for usage example

   'tsw:opsd_human' is a sequence entry in the example protein database
   'tsw'

  Database entry: tsw:opsd_human

ID   OPSD_HUMAN              Reviewed;         348 AA.
AC   P08100; Q16414; Q2M249;
DT   01-AUG-1988, integrated into UniProtKB/Swiss-Prot.
DT   01-AUG-1988, sequence version 1.
DT   13-JUN-2012, entry version 145.
DE   RecName: Full=Rhodopsin;
DE   AltName: Full=Opsin-2;
GN   Name=RHO; Synonyms=OPN2;
OS   Homo sapiens (Human).
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC   Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
OC   Catarrhini; Hominidae; Homo.
OX   NCBI_TaxID=9606;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX   MEDLINE=84272729; PubMed=6589631; DOI=10.1073/pnas.81.15.4851;
RA   Nathans J., Hogness D.S.;
RT   "Isolation and nucleotide sequence of the gene encoding human
RT   rhodopsin.";
RL   Proc. Natl. Acad. Sci. U.S.A. 81:4851-4855(1984).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RA   Suwa M., Sato T., Okouchi I., Arita M., Futami K., Matsumoto S.,
RA   Tsutsumi S., Aburatani H., Asai K., Akiyama Y.;
RT   "Genome-wide discovery and analysis of human seven transmembrane helix
RT   receptor genes.";
RL   Submitted (JUL-2001) to the EMBL/GenBank/DDBJ databases.
RN   [3]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC   TISSUE=Retina;
RX   PubMed=17974005; DOI=10.1186/1471-2164-8-399;
RA   Bechtel S., Rosenfelder H., Duda A., Schmidt C.P., Ernst U.,
RA   Wellenreuther R., Mehrle A., Schuster C., Bahr A., Bloecker H.,
RA   Heubner D., Hoerlein A., Michel G., Wedler H., Koehrer K.,
RA   Ottenwaelder B., Poustka A., Wiemann S., Schupp I.;
RT   "The full-ORF clone resource of the German cDNA consortium.";
RL   BMC Genomics 8:399-399(2007).
RN   [4]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RX   PubMed=15489334; DOI=10.1101/gr.2596504;
RG   The MGC Project Team;
RT   "The status, quality, and expansion of the NIH full-length cDNA
RT   project: the Mammalian Gene Collection (MGC).";
RL   Genome Res. 14:2121-2127(2004).
RN   [5]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-120.
RX   PubMed=8566799; DOI=10.1016/0378-1119(95)00688-5;
RA   Bennett J., Beller B., Sun D., Kariko K.;
RT   "Sequence analysis of the 5.34-kb 5' flanking region of the human
RT   rhodopsin-encoding gene.";


  [Part of this file has been deleted for brevity]

FT                                /FTId=VAR_004816.
FT   VARIANT     209    209       V -> M (effect not known).
FT                                /FTId=VAR_004817.
FT   VARIANT     211    211       H -> P (in RP4; dbSNP:rs28933993).
FT                                /FTId=VAR_004818.
FT   VARIANT     211    211       H -> R (in RP4).
FT                                /FTId=VAR_004819.
FT   VARIANT     216    216       M -> K (in RP4).
FT                                /FTId=VAR_004820.
FT   VARIANT     220    220       F -> C (in RP4).
FT                                /FTId=VAR_004821.
FT   VARIANT     222    222       C -> R (in RP4).
FT                                /FTId=VAR_004822.
FT   VARIANT     255    255       Missing (in RP4).
FT                                /FTId=VAR_004823.
FT   VARIANT     264    264       Missing (in RP4).
FT                                /FTId=VAR_004824.
FT   VARIANT     267    267       P -> L (in RP4).
FT                                /FTId=VAR_004825.
FT   VARIANT     267    267       P -> R (in RP4).
FT                                /FTId=VAR_004826.
FT   VARIANT     292    292       A -> E (in CSNBAD1).
FT                                /FTId=VAR_004827.
FT   VARIANT     296    296       K -> E (in RP4; dbSNP:rs29001653).
FT                                /FTId=VAR_004828.
FT   VARIANT     297    297       S -> R (in RP4).
FT                                /FTId=VAR_004829.
FT   VARIANT     342    342       T -> M (in RP4).
FT                                /FTId=VAR_004830.
FT   VARIANT     345    345       V -> L (in RP4).
FT                                /FTId=VAR_004831.
FT   VARIANT     345    345       V -> M (in RP4).
FT                                /FTId=VAR_004832.
FT   VARIANT     347    347       P -> A (in RP4).
FT                                /FTId=VAR_004833.
FT   VARIANT     347    347       P -> L (in RP4; common variant).
FT                                /FTId=VAR_004834.
FT   VARIANT     347    347       P -> Q (in RP4).
FT                                /FTId=VAR_004835.
FT   VARIANT     347    347       P -> R (in RP4; dbSNP:rs29001566).
FT                                /FTId=VAR_004836.
FT   VARIANT     347    347       P -> S (in RP4; dbSNP:rs29001637).
FT                                /FTId=VAR_004837.
SQ   SEQUENCE   348 AA;  38893 MW;  6F4F6FCBA34265B2 CRC64;
     MNGTEGPNFY VPFSNATGVV RSPFEYPQYY LAEPWQFSML AAYMFLLIVL GFPINFLTLY
     VTVQHKKLRT PLNYILLNLA VADLFMVLGG FTSTLYTSLH GYFVFGPTGC NLEGFFATLG
     GEIALWSLVV LAIERYVVVC KPMSNFRFGE NHAIMGVAFT WVMALACAAP PLAGWSRYIP
     EGLQCSCGID YYTLKPEVNN ESFVIYMFVV HFTIPMIIIF FCYGQLVFTV KEAAAQQQES
     ATTQKAEKEV TRMVIIMVIA FLICWVPYAS VAFYIFTHQG SNFGPIFMTI PAFFAKSAAI
     YNPVIYIMMN KQFRNCMLTT ICCGKNPLGD DEASATVSKT ETSQVAPA
//

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, dasgff, debug, listfile, dbmotif, diffseq,
   draw, restrict, excel, feattable, motif, nametable, regions, seqtable,
   simple, srs, table, tagseq.

   See: http://emboss.sf.net/docs/themes/ReportFormats.html for further
   information on report formats.

   By default pepdigest writes a 'seqtable' report file.

  Output files for usage example

  File: opsd_human.pepdigest

########################################
# Program: pepdigest
# Rundate: Sun 15 Jul 2012 12:00:00
# Commandline: pepdigest
#    -seqall tsw:opsd_human
# Report_format: seqtable
# Report_file: opsd_human.pepdigest
########################################

#=======================================
#
# 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   7129.344 R      Y      TPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPT
GCNLEGFFATLGGEIALWSLVVLAIER
    178     231   6335.517 R      E      YIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPM
IIIFFCYGQLVFTVK
     22      69   5788.894 R      T      SPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLY
VTVQHKKLR
    253     296   5004.103 R      S      MVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIP
AFFAK
    136     177   4600.476 R      Y      YVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAG
WSR
      1      21   2257.506 .      S      MNGTEGPNFYVPFSNATGVVR
    297     311   1728.097 K      Q      SAAIYNPVIYIMMNK
    232     245   1490.547 K      A      EAAAQQQESATTQK
    326     339   1403.466 K      T      NPLGDDEASATVSK
    315     325   1186.483 R      N      NCMLTTICCGK
    340     348    902.957 K      .      TETSQVAPA
    249     252    503.556 K      M      EVTR
    312     314    449.510 K      N      QFR
    246     248    346.384 K      E      AEK

#---------------------------------------
#---------------------------------------

   The header information contains the program 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

   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 to 3, 2 to
   4, etc. In other words, this option will reveal fragments containing
   one potential cut site.

   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. In other words, this option will reveal
   fragments containing one or more potential cut site.

   If the boolean -ragging is specified then terminal digest fragments are
   also shown; this can be useful for mass spectrometry. Ragging is
   further controlled by the -termini option which allows you to select
   removal of residues from the N and/or C termini.

   Each proteolytic enzyme has favoured as well as unfavoured cut sites.
   For example, Trypsin will not normally cut after a K if it is followed
   by (e.g.) another K or a P. By default, only data for favoured cut
   sites is generated. Specifying the qualifier -unfavoured produces data
   for unfavoured cut sites as well.

References

   None.

Warnings

   None.

Diagnostic Error Messages

   None.

Exit status

   It always exits with a status of 0.

Known bugs

   None.

See also

   Program name     Description
   backtranambig    Back-translate a protein sequence to ambiguous nucleotide
                    sequence
   backtranseq      Back-translate a protein sequence to a nucleotide sequence
   compseq          Calculate the composition of unique words in sequences
   emowse           Search protein sequences by digest fragment molecular weight
   freak            Generate residue/base frequency table or plot
   mwcontam         Find weights common to multiple molecular weights files
   mwfilter         Filter noisy data from molecular weights file
   oddcomp          Identify proteins with specified sequence word composition
   pepinfo          Plot amino acid properties of a protein sequence in parallel
   pepstats         Calculate statistics of protein properties
   wordcount        Count and extract unique words in molecular sequence(s)

Author(s)

   Alan Bleasby
   European Bioinformatics Institute, Wellcome Trust Genome Campus,
   Hinxton, Cambridge CB10 1SD, UK

   Please report all bugs to the EMBOSS bug team
   (emboss-bug (c) emboss.open-bio.org) not to the original author.

History

   Written (1999) - Alan Bleasby

   Renamed (2011) from digest to pepdigest to avoid a name clash with
   another utility.

Target users

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

Comments

   None
