OpenMS
DecoyDatabase

Create a decoy peptide database from standard FASTA databases.

Decoy databases are useful to control false discovery rates and thus estimate score cutoffs for identified spectra.

The decoy can either be generated by reversing or shuffling each of the peptides of a sequence (as defined by a given enzyme). For reversing the N and C terminus of the peptides are kept in position by default.

To get a 'contaminants' database have a look at http://www.thegpm.org/crap/index.html or find/create your own contaminant database.

Multiple databases can be provided as input, which will internally be concatenated before being used for decoy generation. This allows you to specify your target database plus a contaminant file and obtain a concatenated target-decoy database using a single call, e.g., DecoyDatabase -in human.fasta crap.fasta -out human_TD.fasta

By default, a combined database is created where target and decoy sequences are written interleaved (i.e., target1, decoy1, target2, decoy2,...). If you need all targets before the decoys for some reason, use only_decoy and concatenate the files externally.

The tool will keep track of all protein identifiers and report duplicates.

Also the tool automatically checks for decoys already in the input files (based on most common pre-/suffixes) and terminates the program if decoys are found.

The command line parameters of this tool are:

DecoyDatabase -- Create decoy sequence database from forward sequence database.
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_DecoyDatabase.html
Version: 3.2.0-pre-nightly-2024-07-19 Jul 20 2024, 02:06:43, Revision: f10e72e
To cite OpenMS:
 + Pfeuffer, J., Bielow, C., Wein, S. et al.. OpenMS 3 enables reproducible analysis of large-scale mass spec
   trometry data. Nat Methods (2024). doi:10.1038/s41592-024-02197-7.

Usage:
  DecoyDatabase <options>

This tool has algorithm parameters that are not shown here! Please check the ini file for a detailed descript
ion or use the --helphelp option

Options (mandatory options marked with '*'):
  -in <file(s)>*                   Input FASTA file(s), each containing a database. It is recommended to incl
                                   ude a contaminant database as well. (valid formats: 'fasta')
  -out <file>*                     Output FASTA file where the decoy database will be written to. (valid form
                                   ats: 'fasta')
  -decoy_string <string>           String that is combined with the accession of the protein identifier to 
                                   indicate a decoy protein. (default: 'DECOY_')
  -decoy_string_position <choice>  Should the 'decoy_string' be prepended (prefix) or appended (suffix) to 
                                   the protein accession? (default: 'prefix') (valid: 'prefix', 'suffix')
  -only_decoy                      Write only decoy proteins to the output database instead of a combined 
                                   database.
  -type <choice>                   Type of sequence. RNA sequences may contain modification codes, which will
                                    be handled correctly if this is set to 'RNA'. (default: 'protein') (valid
                                   : 'protein', 'RNA')
  -method <choice>                 Method by which decoy sequences are generated from target sequences. Note 
                                   that all sequences are shuffled using the same random seed, ensuring that 
                                   identical sequences produce the same shuffled decoy sequences. Shuffled 
                                   sequences that produce highly similar output sequences are shuffled again 
                                   (see shuffle_sequence_identity_threshold). (default: 'reverse') (valid: 
                                   'reverse', 'shuffle')
  -enzyme <enzyme>                 Enzyme used for the digestion of the sample. Only applicable if parameter 
                                   'type' is 'protein'. (default: 'Trypsin') (valid: 'Formic_acid', 'Lys-C', 
                                   'Lys-N', 'Asp-N_ambic', 'Chymotrypsin', 'Chymotrypsin/P', 'CNBr', 'proline
                                   -endopeptidase/HKR', 'Glu-C+P', 'Trypsin', 'Arg-C', 'Arg-C/P', 'Asp-N', 
                                   'Asp-N/B', 'unspecific cleavage', 'Lys-C/P', 'PepsinA', 'TrypChymo', 'Tryp
                                   sin/P', 'V8-DE', 'V8-E', 'leukocyte elastase', 'proline endopeptidase', 
                                   'glutamyl endopeptidase', 'Alpha-lytic protease', '2-iodobenzoate', 'iodos
                                   obenzoate', 'staphylococcal protease/D', 'PepsinA + P', 'cyanogen-bromide'
                                   , 'Clostripain/P', 'elastase-trypsin-chymotrypsin', 'no cleavage')
                                   
Common TOPP 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)

The following configuration subsections are valid:
 - Decoy   Decoy parameters section

You can write an example INI file using the '-write_ini' option.
Documentation of subsection parameters can be found in the doxygen documentation or the INIFileEditor.
For more information, please consult the online documentation for this tool:
  - http://www.openms.de/doxygen/nightly/html/TOPP_DecoyDatabase.html

INI file documentation of this tool:

Legend:
required parameter
advanced parameter
+DecoyDatabaseCreate decoy sequence database from forward sequence database.
version3.2.0-pre-nightly-2024-07-19 Version of the tool that generated this parameters file.
++1Instance '1' section for 'DecoyDatabase'
in[] Input FASTA file(s), each containing a database. It is recommended to include a contaminant database as well.input file*.fasta
out Output FASTA file where the decoy database will be written to.output file*.fasta
decoy_stringDECOY_ String that is combined with the accession of the protein identifier to indicate a decoy protein.
decoy_string_positionprefix Should the 'decoy_string' be prepended (prefix) or appended (suffix) to the protein accession?prefix, suffix
only_decoyfalse Write only decoy proteins to the output database instead of a combined database.true, false
typeprotein Type of sequence. RNA sequences may contain modification codes, which will be handled correctly if this is set to 'RNA'.protein, RNA
methodreverse Method by which decoy sequences are generated from target sequences. Note that all sequences are shuffled using the same random seed, ensuring that identical sequences produce the same shuffled decoy sequences. Shuffled sequences that produce highly similar output sequences are shuffled again (see shuffle_sequence_identity_threshold).reverse, shuffle
shuffle_max_attempts30 shuffle: maximum attempts to lower the amino acid sequence identity between target and decoy for the shuffle algorithm
shuffle_sequence_identity_threshold0.5 shuffle: target-decoy amino acid sequence identity threshold for the shuffle algorithm. If the sequence identity is above this threshold, shuffling is repeated. In case of repeated failure, individual amino acids are 'mutated' to produce a different amino acid sequence.
seed1 Random number seed (use 'time' for system time)
enzymeTrypsin Enzyme used for the digestion of the sample. Only applicable if parameter 'type' is 'protein'.Formic_acid, Lys-C, Lys-N, Asp-N_ambic, Chymotrypsin, Chymotrypsin/P, CNBr, proline-endopeptidase/HKR, Glu-C+P, Trypsin, Arg-C, Arg-C/P, Asp-N, Asp-N/B, unspecific cleavage, Lys-C/P, PepsinA, TrypChymo, Trypsin/P, V8-DE, V8-E, leukocyte elastase, proline endopeptidase, glutamyl endopeptidase, Alpha-lytic protease, 2-iodobenzoate, iodosobenzoate, staphylococcal protease/D, PepsinA + P, cyanogen-bromide, Clostripain/P, elastase-trypsin-chymotrypsin, 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 Overrides tool-specific checkstrue, false
testfalse Enables the test mode (needed for internal use only)true, false
+++DecoyDecoy parameters section
non_shuffle_pattern Residues to not shuffle (keep at a constant position when shuffling). Separate by comma, e.g. use 'K,P,R' here.
keepPeptideNTermtrue Whether to keep peptide N terminus constant when shuffling / reversing.true, false
keepPeptideCTermtrue Whether to keep peptide C terminus constant when shuffling / reversing.true, false