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 from reversed or shuffled sequences.

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.

The command line parameters of this tool are:

DecoyDatabase -- Create decoy protein DB from forward protein DB.
Version: 2.3.0 Jan  9 2018, 17:46:23, Revision: 38ae115

Usage:
  DecoyDatabase <options>

Options (mandatory options marked with '*'):
  -in <file(s)>*                 Input FASTA file(s), each containing a database. It is recommended to includ
                                 e a contaminant database as well. (valid formats: 'fasta')
  -out <file>*                   Output FASTA file where the decoy database will be written to. (valid format
                                 s: 'fasta')
  -decoy_string <string>         String that is combined with the accession of the protein identifier to indi
                                 cate a decoy protein. (default: 'DECOY_')
  -decoy_string_position <enum>  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 datab
                                 ase.
  -method <enum>                 Method by which decoy sequences are generated from target sequences. (defaul
                                 t: 'reverse' valid: 'reverse', 'shuffle')
                                 
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

+DecoyDatabaseCreate decoy protein DB from forward protein DB.

version2.3.0 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

methodreverse Method by which decoy sequences are generated from target sequences.reverse,shuffle

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