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
The command line parameters of this tool are:
INI file documentation of this tool:
OpenMS / TOPP release 2.2.0 | Documentation generated on Tue Aug 29 2017 11:28:57 using doxygen 1.8.13 |