Parameter: decoy_filter


This parameter requires two values. The first value is a short, case-sensitive string of characters that appears in the name of every decoy protein sequence in the database. The second value is either 0 or 1, where 0 indicates these decoy sequences are already provided in the FASTA database supplied by the user, and 1 indicates Kojak should automatically generate the decoy sequences and preface the protein names with the characters supplied in the first value.

If Kojak is requested to generate decoy sequences, it will export the full complement of target and decoy sequences searched in the output directory at the end of analysis.

KOJAK GENERATED DECOYS Kojak generates decoy sequences by reversing the amino acids between enzymatic cleavage sites in the protein sequence. The sites of enzymatic cleavage are determined by the rules supplied with the enzyme parameter. The leading methionine in the sequences, however, remains fixed. This approach ensures that, with very few exceptions, the number, length, and mass of the decoy peptides are identical to the target peptides.
SPECIAL NOTE For Kojak releases prior to version 2.0.0, this parameter only accepted a single decoy filter word. Please note the requirement and purpose of the second, numerical value in the decoy_filter parameter line.


[Text] [Number]


2.0.0 - present


To set the word REV as your decoy sequence label and request Kojak to generate decoy sequences:

decoy_filter = REV 1

To set the word decoy as your decoy sequence label and use the existing decoy-labeled sequences in your FASTA database:

decoy_filter = decoy 0

Deprecated Syntax for versions 1.0 - 1.6.1