Table 1.

A summarized list of major tools available for plant miRNAs, their target identification/prediction and repositories.

Name of the database/resource/repository/tool	Description	Web link	References
TAPIR	Target prediction for Plant miRs	http://bioinformatics.psb.ugent.be/webtools/tapir/	Bonnet et al., 2010
miRTarBase	The experimentally validated miR-target interactions database	http://mirtarbase.mbc.nctu.edu.tw/index.php	Hsu et al., 2011
PMRD	Plant miRNA Database	http://bioinformatics.cau.edu.cn/PMRD/	Zhang et al., 2010
miRanalyzer	miR detection and analysis tool for next-generation sequencing experiments	http://bioinfo5.ugr.es/miRanalyzer/miRanalyzer.php	Hackenberg et al., 2011
PmiRKB	Plant miR Knowledge Base. Four major functional modules, SNPs, Pri-miRs, MiR-Tar and Self-reg, are provided	http://bis.zju.edu.cn/pmirkb/	Meng et al., 2011
miRDeep-P	A computational tool for analyzing the miRtranscriptome in plants	http://faculty.virginia.edu/lilab/miRDP/	Yang and Li, 2011
C-mii	A tool for plant miR and target identification	http://www.biotec.or.th/isl/c-mii	Numnark et al., 2012
Semirna	Searching for plant miRNAs using target sequences	http://www.bioinfocabd.upo.es/semirna/	Muñoz-Mérida et al., 2012
mirTool	A comprehensive web server providing detailed annotation information for known miRs and predicting novel miRs that have not been characterized before	http://centre.bioinformatics.zj.cn/mirtools/	Wu et al., 2013
PASmiR	A literature-curated database for miR molecular regulation in plant response to abiotic stress		Zhang et al., 2013
miRBase	Searchable database of published miR sequences and annotation	http://www.mirbase.org	Kozomara and Griffiths-Jones, 2014
miRPlant	An Integrated Tool for Identification of Plant MiR from RNA Sequencing Data	http://www.australianprostatecentre.org/research/software/mirplant	An et al. (2014)
MTide	An integrated tool for the identification of miR-target interaction in plants	http://bis.zju.edu.cn/MTide/	Zhang et al., 2014b
PNRD	It is an updated version of PMRD	http://structuralbiology.cau.edu.cn/PNRD/index.php	Yi et al., 2015
PlantMirnaT	A miRNA-mRNA integrated analysis system	https://sites.google.com/site/biohealthinformaticslab/resources	Rhee et al., 2015
miRA	Plant miRNA identification tool especially for organisms without existing miRNA annotation. It is also useful for identifying species-specific miRNAs	https://github.com/mhuttner/miRA	Evers et al., 2015
miPEPs	MiRNAs Encode Peptides is a tool for functional analysis of plant miRNA family members		Couzigou et al., 2015
sRNAtoolbox	A set of tools for expression profiling and analysis of sRNA bench results	http://bioinfo5.ugr.es/srnatoolbox	Rueda et al., 2015
miRge	A fast multiplexed method of processing sRNA-sequence data to determine miRNA entropy and identify differential production of miRNA isomiRs	http://atlas.pathology.jhu.edu/baras/miRge.html.	Baras et al., 2015
BioVLAB-MMIA-NGS	MiRNA and mRNA integrated analysis using high-throughput sequencing data coupled with bioinformatics tools.	http://epigenomics.snu.ac.kr/biovlab_mmia_ngs/	Chae et al., 2015
DMD	A dietary miRNA database from 15 dietary plant and animal species	http://sbbi.unl.edu/dmd/	Chiang et al., 2015
WMP	Database for abiotic stress responsive miRNAs in wheat	http://wheat.bioinfo.uqam.ca	Remita et al., 2015
miTRATA	A tool for miRNA truncation and tailing analysis	https://wasabi.dbi.udel.edu/~apps/ta/	Patel et al., 2016
MFSN	A tool for prediction of plant miRNA functions based on functional similarity network (MFSN) through application of transductive multi-label classification (TRAM) to the MFSN		Meng et al., 2016
PlanTE-MIR	Database for transposable element-related plant microRNAs	http://bioinfo-tool.cp.utfpr.edu.br/plantemirdb/	R Lorenzetti et al., 2016
P-SAMS	A Plant Small RNA Maker Site (P-SAMS) is a web tool for artificial miRNAs and synthetic trans-acting small interfering RNAs	http://p-sams.carringtonlab.org	Fahlgren et al., 2016