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               list       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.
   -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.
   -aadata             string     Molecular weight data for amino acids
   -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
-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
-aadata Molecular weight data for amino acids Any string is accepted Eamino.dat
-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

Here is the output from the example:


DIGEST of OPSD_HUMAN from 1 to 348 Molwt= 38892.536

Complete digestion with Trypsin yields 14 fragments:
Start   End     Molwt      Sequence (up to 38 residues)
70      135     7129.324   (R) TPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGP (Y) ...
178     231     6335.500   (R) YIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIP (E) ...
22      69      5788.878   (R) SPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTL (T) ...
253     296     5004.090   (R) MVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTI (S) ...
136     177     4600.464   (R) YVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLA (Y) ...
1       21      2257.500    () MNGTEGPNFYVPFSNATGVVR (S) 
297     311     1728.093   (K) SAAIYNPVIYIMMNK (Q) 
232     245     1490.543   (K) EAAAQQQESATTQK (A) 
326     339     1403.462   (K) NPLGDDEASATVSK (T) 
315     325     1186.480   (R) NCMLTTICCGK (N) 
340     348     902.954    (K) TETSQVAPA  () 
249     252     503.555    (K) EVTR (M) 
312     314     449.509    (K) QFR (N) 
246     248     346.383    (K) AEK (E) 

The first non-blank line is the title containing the name of the program and the name o fthe input sequence with the range considered and the calculated molecular weight of the protein.

The next non-blank line gives the name of the reagent used to digest the protein and the number of fragments reported. The line will report is complete or partial digestion was chosen. If the protein is not digested at all by the reagent chosen the following is reported:

"Is not proteolytically digested using (reagent name)"

If '-overlap' was specified, the next line will be:

"Only overlapping partials shown:"

If '-allpartials' was specified, the next line will be:

"All partials shown:"

The next non-blank line gives the headings of the columns of data.

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