miRNAs are an important class of endogenous small RNAs that regulate gene expression at the post-transcription level. There has been a surge of interest in the past decade in identifying miRNAs and profiling their expression pattern using various experimental approaches. Most recently, deep sequencing of specifically prepared low-molecular weight RNA libraries has been used for both purposes in diverse plant species. A major drawback of these efforts is the exclusive focus on mature miRNA, the final gene product, and ignorance of sequence information associated with other parts of the miRNA genes. New strategies and/or tools are thus highly desirable to analyze the increasingly available sequencing data to gain insights into the miRNA transcriptomes. The development of miRDeep-P, miRDP for short, was motivated by these needs.

Based on ultra deep sampling of small RNA libraries by next generation sequencing, miRDeep-P has two main purposes. First, miRDeep-P can be used to identify miRNA genes in plant species, even for those without detailed annotation. Second, miRDeep-P is designed to assign expression status to individual miRNA genes, which is critical as more miRNAs in plants belong to paralogous families with multiple members encoding identical or near-identical miRNAs.

If you use miRDeep-P in your scientific research, please cite us:

Xiaozeng Yang, Lei Li. 2011 miRDeep-P: a computational tool for analyzing the microRNA transcriptome in plant. Bioinformatics, doi: 10.1093


The miRDeep-P package was developed in Perl by combining the core algorithm of miRDeep, the mapping tool Bowtie, and the Vienna RNA package for predicting RNA secondary structure. It has been tested on two Linux platforms, SUSE 10 and Fedora 14, and should work on similar systems that support Perl.


Four compressed downloads are available here. Two packages, Known_M and New_M, which include the files by which users can reproduce every step and gain familiarity with miRDeep-P. Please note that some of the intermediate files of the New_M are not included due to the size of these files. The users are recommended to run miRDeep-P by these two packages.

1. miRDeep-P1.3.tar.gz includes the core algorithm script and all auxiliary scripts.

2. miRDeep-P1.3 manual includes the details how to use miRDeep-p.

3. Known_M.tar.gz contains the files that we used to explore the expression pattern of annotated miRNA in Arabidopsis.

4. New_M.tar.gz contains the files that we used to find novel miRNAs in Arabidopsis.

All the packages can also be downloaded from miRDeep-P project at (


This work is supported by NSF(DBI-0922526).


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

Also, welcome to join in mail list to discuss issues concerning miRDeep-P.