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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 (upon using the append flag) obtain a concatenated target-decoy database using a single call, e.g., DecoyDatabase -in human.fasta crap.fasta -out human_TD.fasta -append

The command line parameters of this tool are:

DecoyDatabase -- Create decoy peptide databases from normal ones.
Version: 2.0.0 May 16 2015, 09:22:21, Revision: GIT-NOTFOUND

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 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
                                 
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.
version2.0.0 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_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
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

OpenMS / TOPP release 2.0.0 Documentation generated on Sat May 16 2015 16:13:42 using doxygen 1.8.9.1