Journal Article

Automatic identification of species-specific repetitive DNA sequences and their utilization for detecting microbial organisms

Triinu Koressaar, Kai Jõers and Maido Remm

in Bioinformatics

Volume 25, issue 11, pages 1349-1355
Published in print June 2009 | ISSN: 1367-4803
Published online April 2009 | e-ISSN: 1460-2059 | DOI:

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Motivation: The concentration of pathogen DNA in biological samples is often very low. Therefore, the sensitivity of diagnostic tests is always a critical factor.

Results: We have developed a novel computational method that identifies species-specific repeats from microbial organisms and automatically designs species-specific PCR primers for these repeats. We tested the methodology on 30 randomly chosen microbial species and we demonstrate that species-specific repeats longer than 300 bp exist in all these genomes. We also used our methodology to design species-specific PCR primers for 86 repeats from five medically relevant microbial species. These PCR primers were tested experimentally. We demonstrate that using species-specific repeats as a PCR template region can increase the sensitivity of PCR in diagnostic tests.

Availability and Implementation: A web version of the method called MultiMPrimer3 was implemented and is freely available at


Supplementary information: Supplementary data are available at Bioinformatics online.

Journal Article.  4999 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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