Translational Research


An Integrated Tool for Identification of Plant MiRNA from RNA Sequencing Data

Small RNA sequencing has been commonly used to identify novel miRNAs and their expression levels in plants. There are several miRNA identification tools for animals such as miRDeep, miRDeep2 and miRDeep*. miRDeep-P was developed from miRDeep for plants using miRDeep’s probabilistic model of miRNA biogenesis. However, it is necessary to use a different strategy to find suitable hairpin regions in the plant genome since plant miRNAs have much longer precursor miRNA than those in animal. Thus, we have developed miRPlant which extends miRDeep* to various plant species by adopting suitable strategies to identify hairpin excision regions and hairpin structure filtering for plants. Similar to miRDeep*, miRPlant does not require any third party tools such as mapping or RNA secondary structure prediction tools. In addition, miRPlant uses a graphic user interface for data input and output, and identified miRNA is displayed with all RNAseq reads in a hairpin diagram. This tool can be easily used by biologists without much computer knowledge.

miRPlant interface


new version in sourceforge http://sourceforge.net/projects/mirplant



Permission to use this work is granted under the  GNU Lesser General Public License (LGPL).


For enquiries about the software please contact Jiyuan An (j.an@qut.edu.au) or Colleen Nelson (colleen.nelson@qut.edu.au)
Tel: +61 7 3443 7280

Related tools

miRDeep*, miRDeep-P, miRDeepFinder, miR-PREFeR, miRDeep2, miRTRAP, MIReNA, miRanalyzer. miRNAkey, miRTools, SeqBuster, CPSS, miRGator, targetScan, picard, samtools, miRspring, miRdentify

Citing miRPlant

An J, Lai J, Sajjanhar A, Lehman ML, Nelson CC: miRPlant: an integrated tool for identification of plant miRNA from RNA sequencing data. BMC bioinformatics 2014, 15(1):275.