{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,5]],"date-time":"2025-11-05T06:14:38Z","timestamp":1762323278397},"reference-count":37,"publisher":"Oxford University Press (OUP)","issue":"11","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":2734,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009,6,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: The concentration of pathogen DNA in biological samples is often very low. Therefore, the sensitivity of diagnostic tests is always a critical factor.<\/jats:p>\n               <jats:p>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.<\/jats:p>\n               <jats:p>Availability and Implementation: A web version of the method called MultiMPrimer3 was implemented and is freely available at http:\/\/bioinfo.ut.ee\/multimprimer3\/.<\/jats:p>\n               <jats:p>Contact: \u00a0maido.remm@ut.ee<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp241","type":"journal-article","created":{"date-parts":[[2009,4,9]],"date-time":"2009-04-09T01:09:00Z","timestamp":1239239340000},"page":"1349-1355","source":"Crossref","is-referenced-by-count":18,"title":["Automatic identification of species-specific repetitive DNA sequences and their utilization for detecting microbial organisms"],"prefix":"10.1093","volume":"25","author":[{"given":"Triinu","family":"Koressaar","sequence":"first","affiliation":[{"name":"1 Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Riia str. 23, Tartu 51010 and 2Quattromed HTI\u00ae Laborid, Nooruse 9, Tartu 50411, Estonia"}]},{"given":"Kai","family":"J\u00f5ers","sequence":"additional","affiliation":[{"name":"1 Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Riia str. 23, Tartu 51010 and 2Quattromed HTI\u00ae Laborid, Nooruse 9, Tartu 50411, Estonia"}]},{"given":"Maido","family":"Remm","sequence":"additional","affiliation":[{"name":"1 Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Riia str. 23, Tartu 51010 and 2Quattromed HTI\u00ae Laborid, Nooruse 9, Tartu 50411, Estonia"}]}],"member":"286","published-online":{"date-parts":[[2009,4,8]]},"reference":[{"key":"2023013111504392600_B1","doi-asserted-by":"crossref","first-page":"2280","DOI":"10.1093\/oxfordjournals.molbev.a003774","article-title":"Study of intrachromosomal duplications among the eukaryote genomes","volume":"18","author":"Achaz","year":"2001","journal-title":"Mol. 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