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

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/).