MiPRIME: An integrated and intelligent platform for mining primer and probe sequences of microbial species

Accurately detecting pathogenic microorganisms requires effective primers and probe designs. Literature-derived primers are a valuable resource as they have been tested and proven effective in previous research. However, manually mining primers from published texts is time-consuming and limited in species scop.

To address these challenges, we have developed MiPRIME, a real-time Microbial Primer Mining platform for primer/probe sequences extraction of pathogenic microorganisms with three highlights: i) Comprehensive integration. Covering more than 40 million articles and 548,942 organisms, the platform enables high-frequency microbial gene discovery from a global perspective, facilitating user-defined primer design and advancing microbial research. ii) Employing a BioBERT-based text mining model with 98.02% accuracy, greatly reducing information processing time. iii) using a primer ranking score, PR_score, for intelligent recommendation of species-specific primers. Overall, MiPRIME is a practical tool for primer mining in the pan-microbial field, saving time and cost of trial-and-error experiments.

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Supplementary data are available at Bioinformatics online.