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:
INI file documentation of this tool:
OpenMS / TOPP release 1.11.1 | Documentation generated on Mon Aug 18 2014 14:41:10 using doxygen 1.8.7 |