DecoyDatabase

Create decoy peptide databases from normal ones.

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.

The command line parameters of this tool are:

DecoyDatabase -- Create decoy peptide databases from normal ones.
Version: 1.10.0 Mar  7 2013, 08:30:22, Revision: unknown

Usage:
  DecoyDatabase <options>

Options (mandatory options marked with '*'):
  -in <file>*                    Input FASTA file containing the database. (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 appended to the accession of the protein database to indicate
                                 a decoy protein. (default: '_rev')
  -decoy_string_position <enum>  Should the 'decoy_string' be prepended (prefix) or appended (suffix) to the 
                                 protein accession? (default: 'suffix' valid: 'prefix', 'suffix')
  -append                        If this flag is used, the decoy database is appended to the target database,
                                 allowing combined target decoy searches.
  -shuffle                       If 'true' then the decoy hit are shuffled from the target sequences, otherwi
                                 se they are reversed
  -contaminants <file>           Input a FASTA file containing contaminants - if given they are included in 
                                 the database (recommended) (valid formats: 'fasta')
                                 
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 peptide databases from normal ones.

version1.10.0 Version of the tool that generated this parameters file.

++1Instance '1' section for 'DecoyDatabase'

in Input FASTA file containing the database.input file*.fasta

out Output FASTA file where the decoy database will be written to.output file*.fasta

decoy_string_rev String that is appended to the accession of the protein database to indicate a decoy protein.

decoy_string_positionsuffix Should the 'decoy_string' be prepended (prefix) or appended (suffix) to the protein accession?prefix,suffix

appendfalse If this flag is used, the decoy database is appended to the target database, allowing combined target decoy searches.true,false

shufflefalse If 'true' then the decoy hit are shuffled from the target sequences, otherwise they are reversedtrue,false

contaminants Input a FASTA file containing contaminants - if given they are included in the database (recommended)input file*.fasta

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

testfalse Enables the test mode (needed for internal use only)true,false