deBruijn

The project takes target database (.fasta) file as input and generates a de Bruijn decoy (.fasta) file and a target+decoy concatenated (.fasta) file.

de Bruijn decoy parameters

Options:

Required argument:

• --input <.fasta>

Optional arguments:

• [--output <.fasta>]

• [--k <integer value greater than 0>] (default: 2)

• [--enzyme 0/1/2] (0=non specific, 1=trypsin (default), 2=chymotrypsin)

• [--compositoin 0/1/2] (0=not adaptive, target composition not considered, 1=not adaptive, target composition considered, 2=adaptive, target composition consodered (default))

Running de Bruijn decoy generator

• Download the ZIP file and unzip deBruijn-master.zip (NB: Saving the .jar file using save link as ... may result in a corrupted .jar file.)

• Run: java -jar "DIRECTORY OF THE DEBRUIJN-MASTER/deBruijn.jar --input <*.fasta> [optional arguments]"