Digestor

Digests a protein database in-silico.

pot. predecessor tools	$\longrightarrow$ Digestor $\longrightarrow$	pot. successor tools
none (FASTA input)	$\longrightarrow$ Digestor $\longrightarrow$	IDFilter (peptide blacklist)

This application is used to digest a protein database to get all peptides given a cleavage enzyme. At the moment only trypsin is supported.

The output can be used as a blacklist filter input to IDFilter, to remove certain peptides.

Note: Currently mzIdentML (mzid) is not directly supported as an input/output format of this tool. Convert mzid files to/from idXML using IDFileConverter if necessary.

The command line parameters of this tool are:

Digestor -- Digests a protein database in-silico.
Version: 2.3.0 Jan  9 2018, 17:46:23, Revision: 38ae115

Usage:
  Digestor <options>

Options (mandatory options marked with '*'):
  -in <file>*                 Input file (valid formats: 'fasta')
  -out <file>*                Output file (peptides) (valid formats: 'idXML', 'fasta')
  -out_type <type>            Set this if you cannot control the filename of 'out', e.g., in TOPPAS. (valid: 
                              'idXML', 'fasta')
  -missed_cleavages <number>  The number of allowed missed cleavages (default: '1' min: '0')
  -min_length <number>        Minimum length of peptide (default: '6')
  -max_length <number>        Maximum length of peptide (default: '40')
  -enzyme <string>            The type of digestion enzyme (default: 'Trypsin' valid: 'Lys-N', 'Asp-N', 'Tryp
                              sin', 'V8-E', 'Alpha-lytic protease', 'leukocyte elastase', 'Trypsin/P', '2-iod
                              obenzoate', 'no cleavage', 'unspecific cleavage', 'Arg-C/P', 'Lys-C/P', 'Chymot
                              rypsin/P', 'Asp-N_ambic', 'Chymotrypsin', 'Formic_acid', 'proline endopeptidase
                              ', 'glutamyl endopeptidase', 'PepsinA', 'TrypChymo', 'Arg-C', 'V8-DE', 'CNBr',
                              'Asp-N/B', 'Lys-C')
                              
Common UTIL options:
  -ini <file>                 Use the given TOPP INI file
  -threads <n>                Sets the number of threads allowed to be used by the TOPP tool (default: '1')
  -write_ini <file>           Writes the default configuration file
  --help                      Shows options
  --helphelp                  Shows all options (including advanced)

INI file documentation of this tool:

Legend:

required parameter

advanced parameter

+DigestorDigests a protein database in-silico.

version2.3.0 Version of the tool that generated this parameters file.

++1Instance '1' section for 'Digestor'

in input fileinput file*.fasta

out Output file (peptides)output file*.idXML,*.fasta

out_type Set this if you cannot control the filename of 'out', e.g., in TOPPAS.idXML,fasta

missed_cleavages1 The number of allowed missed cleavages0:∞

min_length6 Minimum length of peptide

max_length40 Maximum length of peptide

enzymeTrypsin The type of digestion enzymeTrypChymo,Trypsin/P,Arg-C/P,Lys-C/P,unspecific cleavage,Chymotrypsin/P,leukocyte elastase,proline endopeptidase,V8-DE,V8-E,glutamyl endopeptidase,PepsinA,Arg-C,Formic_acid,CNBr,Trypsin,Lys-C,Lys-N,Asp-N,Asp-N/B,Chymotrypsin,Asp-N_ambic,Alpha-lytic protease,2-iodobenzoate,no cleavage

log Name of log file (created only when specified)

debug0 Sets the debug level

threads1 Sets the number of threads allowed to be used by the TOPP tool

no_progressfalse Disables progress logging to command linetrue,false

forcefalse Overwrite tool specific checks.true,false

testfalse Enables the test mode (needed for internal use only)true,false