%0 Journal Article
%T MiPRIME: an integrated and intelligent platform for mining primer and probe sequences of microbial species.
%A Zhang Z
%A Ren J
%A Ren L
%A Zhang L
%A Ai Q
%A Long H
%A Ren Y
%A Yang K
%A Feng H
%A Li S
%A Li X
%J Bioinformatics
%V 40
%N 7
%D 2024 Jul 1
%M 38954836
%F 6.931
%R 10.1093/bioinformatics/btae429
%X BACKGROUND: 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.
RESULTS: 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 >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) Using a BioBERT-based text mining model with 98.02% accuracy, greatly reducing information processing time. (iii) Using a primer ranking score, PRscore, 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.
METHODS: The web is available at {{https://www.ai-bt.com}}.