Representational difference analysis: critical appraisal and method development for the identification of unique DNA sequences from prokaryotes
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Updated: Aug 31, 2026

Identification of Rare Bacterial Pathogens by 16S rRNA Gene Sequencing and MALDI-TOF MS
Published on: July 11, 2016
Natalie L Allen1, Charles W Penn, Anthony C Hilton
1School of Biosciences, The University of Birmingham, Edgbaston, B15 2TT, Birmingham, UK.
Abstract:
Representational difference analysis (RDA) has great potential for preferential amplification of unique but uncharacterised DNA sequences present in one source such as a whole genome, but absent from a related genome or other complex population of sequences. While a few examples of its successful exploitation have been published, the method has not been well dissected and robust, detailed published protocols are lacking. Here we examine the method in detail, suggest improvements and provide a protocol that has yielded key unique sequences from a pathogenic bacterial genome.
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