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percolator edited this page Sep 13, 2010 · 3 revisions

An easy and effective way to implement a null model for the peptide identification problem within mass spectrometry is to use so called decoy databases, that is randomized versions of the target database. Many users prefer to reverse the sequences in the target database, others prefer to shuffle their data: The advantage of reversed copies of a database is that that action will conserve homologies, however shuffling enables users to generate more than one single decoy data base.

Mimic combines the advantages of both methods by shuffling peptides in a manner that conserves homolog peptides. The method first identifies all homolog peptides, shuffles the unique peptides and then redistributes them to each protein again again. In this way a set of peptides that are homologs before shuffling will be homologs after shuffling as well.

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