Digests a protein database in-silico.
| pot. predecessor tools | Digestor | pot. successor tools |
| none (FASTA input) | 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.
The command line parameters of this tool are:
Digestor -- Digests a protein database in-silico.
Version: 1.11.1 Nov 14 2013, 11:18:15, Revision: 11976
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: 'Trypsin', 'none')
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:
| OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:24 using doxygen 1.8.5 |