ArticleBioinformatics (Oxford, England)2009
Automatic identification of species-specific repetitive DNA sequences and their utilization for detecting microbial organisms.
Article in Bioinformatics (Oxford, England), 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
8 citing papers in PubMed.
- Article
- Outer Membrane Vesicles (OMVs) as Biomedical Tools and Their Relevance as Immune-Modulating Agents againstInternational journal of molecular sciences · 2023Review
- Shine: A novel strategy to extract specific, sensitive and well-conserved biomarkers from massive microbial genomic datasets.BMC bioinformatics · 2023Article
- Population Genetic Analyses ofFrontiers in microbiology · 2021Article
- Laboratory Methods in Molecular Epidemiology: Bacterial Infections.Microbiology spectrum · 2018Review
- Development and first evaluation of a novel multiplex real-time PCR on whole blood samples for rapid pathogen identification in critically ill patients with sepsis.European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology · 2018Article
- Primer3--new capabilities and interfaces.Nucleic acids research · 2012Article
- Characterization of species-specific repeats in 613 prokaryotic species.DNA research : an international journal for rapid publication of reports on genes and genomes · 2012Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationThe concentration of pathogen DNA in biological samples is often very low. Therefore, the sensitivity of diagnostic tests is always a critical factor.
resultsWe 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/).
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Registered trials
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