Digests a protein database in-silico.
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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.
Digestor -- Digests a protein database in-silico. Version: 2.0.0 Aug 25 2015, 00:02:58, Revision: GIT-NOTFOUND 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 2.0.0 | Documentation generated on Tue Aug 25 2015 05:53:56 using doxygen 1.8.9.1 |