OpenMS  2.6.0
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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 obtain a concatenated target-decoy database using a single call, e.g., DecoyDatabase -in human.fasta crap.fasta -out human_TD.fasta

By default, a combined database is created where target and decoy sequences are written interleaved (i.e., target1, decoy1, target2, decoy2,...). If you need all targets before the decoys for some reason, use only_decoy and concatenate the files externally.

The tool will keep track of all protein identifiers and report duplicates.

The command line parameters of this tool are:

INI file documentation of this tool: