Shine: To explore specific, sensitive and conserved biomarkers from massive microbial genomic data within intrapopulations

Abstract

AbstractBackgroundTo improve the quality of nucleic acid detection reagents, we provided a new strategy, Shine, to explore specific, sensitive and conserved biomarkers from massive microbial genomic data within intrapopulations in order to improve detection sensitivity and accuracy. It is obvious that the more comprehensive genomic data are, the more effective the detection biomarkers.ResultsWe demonstrated that our method could detect undiscovered multicopy conserved species-specific or even subspecies-specific target fragments, according to several clinical projects. In particular, this approach was effective for any pathogenic microorganism even in incompletely assembled motifs. Based on our strategy, the detection device designed with quantitative PCR primers and probes for systematic and automated detection of pathogenic microorganisms in biological samples may cover all pathogenic microorganisms without limits based on genome annotation. On the website https://bioinfo.liferiver.com.cn, users may select different configuration parameters depending on the purpose of the project to realize routine clinical detection practices.ConclusionsIt is recommended that our strategy is suitable to identify shared universal phylogenetic markers with few false positive or false negative errors and to automate the design of minimal primers and probes to detect pathogenic communities with cost-effective predictive power.