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. 2014 Aug 12;15(1):275.
doi: 10.1186/1471-2105-15-275.

miRPlant: an integrated tool for identification of plant miRNA from RNA sequencing data

Jiyuan An  1 , John Lai, Atul Sajjanhar, Melanie L Lehman, Colleen C Nelson
Affiliations

miRPlant: an integrated tool for identification of plant miRNA from RNA sequencing data

Jiyuan An et al. BMC Bioinformatics. .

Abstract

Background: Small RNA sequencing is commonly used to identify novel miRNAs and to determine their expression levels in plants. There are several miRNA identification tools for animals such as miRDeep, miRDeep2 and miRDeep*. miRDeep-P was developed to identify plant miRNA using miRDeep's probabilistic model of miRNA biogenesis, but it depends on several third party tools and lacks a user-friendly interface. The objective of our miRPlant program is to predict novel plant miRNA, while providing a user-friendly interface with improved accuracy of prediction.

Result: We have developed a user-friendly plant miRNA prediction tool called miRPlant. We show using 16 plant miRNA datasets from four different plant species that miRPlant has at least a 10% improvement in accuracy compared to miRDeep-P, which is the most popular plant miRNA prediction tool. Furthermore, miRPlant uses a Graphical User Interface for data input and output, and identified miRNA are shown with all RNAseq reads in a hairpin diagram.

Conclusions: 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. miRPlant does not require any third party tools such as mapping or RNA secondary structure prediction tools. miRPlant is also the first plant miRNA prediction tool that dynamically plots miRNA hairpin structure with small reads for identified novel miRNAs. This feature will enable biologists to visualize novel pre-miRNA structure and the location of small RNA reads relative to the hairpin. Moreover, miRPlant can be easily used by biologists with limited bioinformatics skills.miRPlant and its manual are freely available at http://www.australianprostatecentre.org/research/software/mirplant or http://sourceforge.net/projects/mirplant/.

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Figures

Figure 1
Figure 1
Output display of predicted miRNA. The read location and number of reads are shown relative to the precursor hairpin structure. The red sequence represents the mature miRNA.
Figure 2
Figure 2
Parameter settings for miRPlant. Adapter sequences need to be replaced as appropriate. Data processing by miRPlant depends on the extension of the input file. Mapping and identification is performed if the input file extension is “.fastq” or “.fa”. Only identification is performed if the file extension is “.bam”. Output “.result” files are shown after clicking “submit”.
See this image and copyright information in PMC

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