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: 1.11.1 Nov 14 2013, 11:18:15, Revision: 11976 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:
OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:24 using doxygen 1.8.5 |