MicroRNAs (miRNAs) are ~21-nucleotide endogenous small RNAs (sRNAs) that regulate gene expression at the post-transcription level. Many pieces of research have been carried out to identify miRNAs and study their functions in the last decade, especially after next generation sequencing (NGS) methods introduced. By various computational tools, a large number of plant miRNAs are identified. However, many of them are questionable, potentially false-positives. Thus, how to minimize false-positive miRNAs becomes a big challenge. With more and more complex and large plant genomes sequenced, how to fast analyze miRNA transcriptome in these plants turns into another big challenge. The development of miRDeep-P2, miRDP2 for short, was motivated by these needs.

miRDP2 is adopted from miRDeep-P (miRDP) with new strategies and overhauled algorithm. We have tested miRDP2 to analyze miRNA transcriptomes in such plants with gradually increased genome size as Arabidopsis, rice, tomato, maize and wheat. Compared with miRDeep-P and several other computational tools, miRDP2 processed very fast. By incorporating newly updated plant miRNA annotation criteria, the accuracy of miRDP2 is also improved. Our results demonstrate miRDP2 as a fast and accurate tool for analyzing the miRNA transcriptome in plants.

If you use miRDP2 in your scientific research, please cite us:

Zheng Kuang, Ying Wang, Lei Li and Xiaozeng Yang. 2018. Bioinformatics. miRDeep-P2: accurate and fast analysis of the microRNA transcriptome in plants.


The miRDP2 package was developed in Perl, the mapping tool Bowtie, and the Vienna RNA package for predicting RNA secondary structure. It has been tested on multiple Linux platforms, including SUSE 12 and Fedora 28, and should work on similar systems that support Perl.


All the packages, including latest version, user manual and tested datasets, can be downloaded from miRDP2 project at ( Please note that some of the intermediate files are not included due to the size of these files. The users are recommended to run miRDP2 by tested datasets for gaining familiarity with miRDP2.


This work is supported by BAAFS (KJCX20180425 and KJCX20180204) to XY and NSFC (31621001) to LL.


Comments and suggestions are welcomed. If you meet any troubles or find any bugs when you use miRDP2, please email to

Also, welcome to join in to discuss issues concerning miRDP2.