OpenMS
2.5.0
|
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.
The output can be used e.g. 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. Full documentation: http://www.openms.de/documentation/UTILS_Digestor.html Version: 2.5.0-nightly-2020-03-06 Mar 7 2020, 01:22:16, Revision: 84b1398 To cite OpenMS: Rost HL, Sachsenberg T, Aiche S, Bielow C et al.. OpenMS: a flexible open-source software platform for mass spectrometry data analysis. Nat Meth. 2016; 13, 9: 741-748. doi:10.1038/nmeth.3959. 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: 'Arg-C/P', '2-iodobenz oate', 'iodosobenzoate', 'staphylococcal protease/D', 'proline-endopeptidase/H KR', 'Glu-C+P', 'PepsinA + P', 'cyanogen-bromide', 'Clostripain/P', 'elastase- trypsin-chymotrypsin', 'no cleavage', 'unspecific cleavage', 'Trypsin', 'Chymo trypsin', 'Chymotrypsin/P', 'V8-E', 'leukocyte elastase', 'proline endopeptida se', 'glutamyl endopeptidase', 'Alpha-lytic protease', 'Asp-N', 'Asp-N/B', 'Lys-N', 'Lys-C/P', 'PepsinA', 'CNBr', 'Formic_acid', 'Lys-C', 'TrypChymo', 'Trypsin/P', 'V8-DE', 'Arg-C', 'Asp-N_ambic') Options for FASTA output files: -FASTA:ID <option> Identifier to use for each peptide: copy from parent protein (parent); a conse cutive number (number); parent ID + consecutive number (both) (default: 'paren t' valid: 'parent', 'number', 'both') -FASTA:description <option> Keep or remove the (possibly lengthy) FASTA header description. Keeping it can increase resulting FASTA file significantly. (default: 'remove' valid: 'remove', 'keep') 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: