Table 1: Major Plant databases providing information on the miR and their targets.

Name

Description

Link

miRBase

Searchable database of published miR sequences and annotation

http://www.mirbase.org

deepBase

Database for annotating and discovering small and long ncRNAs (miRs, siRNAs, piRNAs) from high-throughput deep sequencing data.

http://deepbase.sysu.edu.cn/

PMRD

Database involving miRs and their target genes, especially model plants and major crops

http://bioinformatics.cau.edu.cn/PMRD/

PNRD

It is an updated version of PMRD

http://structuralbiology.cau.edu.cn/PNRD/index.php

PMTED

Plant miR Expression Database

http://pmted.agrinome.org/

Plant MPSS

Measure’s the expression level of most genes (including

sRNA and their targets) under defined conditions and provide information about potentially novel transcripts. with the help of public HTS data

 

http://mpss.udel.edu/

miRTarBase

The experimentally validated miR-target interactions databaseA resource for predicted miR targets and expression

http://mirtarbase.mbc.nctu.edu.tw/

Rfam

A resource for predicted miR targets and expression

http://rfam.xfam.org/

 

 

 

 

ARMOUR

A Rice miRNA: mRNA Interaction Resource

http://armour.icgeb.trieste.it/

 

TABLE 2: Major tools for analyzing plant miRs and their targets.

Name

Description

Link

PASmiR

A literature-curated database for miR molecular regulation in plant response to abiotic stress

http://pcsb.ahau.edu.cn:8080/ PASmiR/

isomiRex

Web portal to identify miRs and their isoforms as well as differential expression of NGS datasets

http://bioinfo1.uni-plovdiv.bg/ isomiRex/

CLC genomics Workbench

Analyze, compares and visualizes NGS data

http://www.clcbio.com/products/clcgenomicsworkbench/

miRTarBase

The experimentally validated miR-target interactions database

http://mirtarbase.mbc.nctu.edu.tw/ index.php

MIRFINDER

Computational pre-miR prediction tool

http://www.bioinformatics.org/ mirfinder/

Targetfinder

Predicts small RNA targets in a sequence database using a plant-based scoring metric

http://carringtonlab.org/resources/ targetfinder

mirCheck

A PERL script designed to identify RNA sequences with secondary structures similar to plant miRs

http://bartellab.wi.mit.edu/software. html

findmiRNA

Predicts potential miRs within candidate precursor sequences that have corresponding target sites within transcripts

http://sundarlab.ucdavis.edu/mirna/

MicroInspector

A web tool for detection of miR binding sites in a RNA sequence

http://bioinfo.uni-plovdiv.bg/ microinspector/

RNAhybrid

Calculates a minimal free energy hybridization of RNA sequence(s) and miR(s)

http://bibiserv2.cebitec.uni-bielefeld. de/rnahybrid/

CleaveLand

A pipeline for using degradome data to find cleaved small RNA targets

http://axtell-lab-psu.weebly.com/ cleaveland.html

TAPIR

Target prediction for Plant miRs

http://bioinformatics.psb.ugent.be/ webtools/tapir/

psRNATarget

A plant sRNA target analysis server

http://plantgrn.noble.org/ psRNATarget/

miRanalyzer

miR detection and analysis tool for next-generation sequencing experiments

http://bioinfo5.ugr.es/miRanalyzer/ miRanalyzer.php

PmiRKB

Plant miR knowledge base includes the miRs of two model plantsArabidopsis and rice. Four major functional modules, SNPs, Pri-miRs, MiR-Tar and Self-reg, are provided

http://bis.zju.edu.cn/pmirkb/

miRDeep-P

A computational tool for analyzing the miR transcriptome in plants

http://faculty.virginia.edu/lilab/miRDP/

C-mii

A tool for plant miR and target identification

http://www.biotec.or.th/isl/c-mii

Semirna

Searching for plant miRNAs using target sequences

http://www.bioinfocabd.upo.es/

semirna/

UEA sRNA Workbench

A suite of tools for analysing and visualizing NGS datasets

http://srna-workbench.cmp.uea.ac. uk/

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/

miRPlant

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

http://www.australianprostatecentre. org/research/software/mirplant

MTide

An integrated tool for the identification of miR-target interaction in plants

http://bis.zju.edu.cn/MTide/