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Bioinformatics Advance Access originally published online on April 8, 2009
Bioinformatics 2009 25(11):1349-1355; doi:10.1093/bioinformatics/btp241
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© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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

Triinu Koressaar 1, Kai Jõers 2 and Maido Remm 1,*

1Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Riia str. 23, Tartu 51010 and 2Quattromed HTI® Laborid, Nooruse 9, Tartu 50411, Estonia

*To whom correspondence should be addressed.


  Abstract

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 http://bioinfo.ut.ee/multimprimer3/.

Contact: maido.remm{at}ut.ee

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Alex Bateman

Received on January 16, 2009; revised on March 16, 2009; accepted on April 3, 2009

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