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Bioinformatics. 2019 Jul 15;35(14):2521-2522. doi: 10.1093/bioinformatics/bty972.

miRDeep-P2: accurate and fast analysis of the microRNA transcriptome in plants.

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Beijing Agro-biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China.
Peking-Tsinghua Center for Life Sciences, School of Advanced Agricultural Sciences and School of Life Sciences, Peking University, Beijing, China.



Two major challenges arise when employing next-generation sequencing methods to comprehensively identify microRNAs (miRNAs) in plants: (i) how to minimize the false-positive inheritable to computational predictions and (ii) how to minimize the computational time required for analyzing the miRNA transcriptome in plants with complex and large genomes.


We updated miRDeep-P to miRDeep-P2 (miRDP2) by employing a new filtering strategy and overhauling the algorithm. miRDP2 has been tested against miRNA transcriptomes in plants with increasing genome sizes that included Arabidopsis, rice, tomato, maize and wheat. Compared with miRDeep-P and several other computational tools, miRDP2 processes next-generation sequencing data with superior speed. By incorporating newly updated plant miRNA annotation criteria and developing a new scoring system, the accuracy of miRDP2 outperformed other programs. Taken together, our results demonstrate miRDP2 as a fast and accurate tool for analyzing the miRNA transcriptome in plants.


The miRDP2 are freely available from


Supplementary data are available at Bioinformatics online.

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