Decoy Database Builder

Introduction to the use of the Decoy Database Builder

The false positive rate of protein searches can be estimated by searching decoy databases containing entries with 'right' (original / source) and 'false' (decoy) protein sequences. The false positive rate of a protein identification is defined as the quotient of the number of erroneous identified proteins (from the decoy part) and the sum of the number of all correctly identified proteins (from the source part) and the number of all erroneous identified proteins.

Decoy databases can be created from Fasta formatted protein database files in different ways:


Graphical user interface

Command line interface

If you want to run the software in a larger bioinformatics infrastructure then the DecoyDBB can now be called from within batch scripts. The syntax for generating decoy databases is as follows:

java -jar DecoyDBB filename decoytype append masstolerance

Formatting rules


in case of any question do not hesitate to contact