Kojak Instruction Manual
Kojak is operated from the command line on both Windows and Linux systems. Prior to Kojak analysis, data files must be converted to standard open formats (exception: Thermo RAW files on Windows), and a sequence database must be generated, with decoy sequences, for the proteins to be searched.
Specific details for setting up, running, and interpreting results from Kojak are in development. Until then, please refer to the Quick Start Guide.