TABLE 1: Computational tools for identification for miRNAs using deep sequencing data

Name

Description

Link

PNRD (DB)

It is an updated version of PMRD, involving miRs and their target genes

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

miRDeepFinder

Asoftware package developed to identify and functionally analyze plant miRNAs

http://www.leonxie.com/DeepFinder.php

miRNEST 2.0 (DB)

A comprehensive database of animal, plant and virus microRNAs

http://mirnest.amu.edu.pl

miRspring

A new way of sharing and analysing sequencing data for small RNA.

http://mirspring.victorchang.edu.au

mirTools 2.0

Tool for non-coding RNA discovery, profiling, and functional annotation based on high-throughput sequencing

 

122.228.158.106/mr2_dev

miRDeep*

An integrated application tool for miRNA identification from RNA sequencing data.

 http://www.australianprostatecentre.org/research/software/mirdeep-star

miRExpress

A software package implemented for generating miRNA expression profiles from high-throughput sequencing of RNA without the need for sequenced genomes.

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

miRanalyzer

A microRNA detection and analysis tool for next-generation sequencing experiments.

http://web.bioinformatics.cicbiogune.es/microRNA/

miRNAkey

A software pipeline for the analysis of microRNA Deep Sequencing data.

 http://ibis.tau.ac.il/miRNAkey/

µPC

Online resource that enables users to comprehensively compare and predict plant miRNAs and their targets

http://www3a.biotec.or.th/micropc/

 

TABLE 2: Computational tools for miRNA target prediction

Name

Description

Link

psRNATarget

A plant small RNA target analysis server

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

PNRD

a plant non-coding RNA database

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

TAPIR

A web server for the prediction of plant microRNA targets including target mimics

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

miRTour

Plant miRNA and target prediction tool

http://bio2server.bioinfo.uni-plovdiv.bg/miRTour/

Target-align

a Smith-Waterman-like alignment tool in order to accurately predict miRNA targets

http://www.leonxie.com/targetAlign.php

miRDB

An online resource for miRNA target prediction and functional annotations

http://mirdb.org/miRDB/

MicroInspector

 web tool for detection of miRNA binding sites in an RNA sequence

http://www.imbb.forth.gr/microinspector

 

 

TABLE 3: Computational tools for miRNA target expression

Name

Description

Link

PMTED

A Plant MiRNA Target Expression Database to study the miRNA functions by inferring their target gene expression profiles 

http://pmted.agrinome.org/

PNRD

It is the updated version of PMRD. PNRD mainly focuses on plant species miRNA expression profiles

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

Mfold

Web server for prediction of RNA secondary structure by energy minimization

http://unafold.rna.albany.edu/?q=mfold/

RANfold

web server to predict secondary structures of single stranded RNA or DNA sequences

http://rna.tbi.univie.ac.at/cgi-bin/RNAfold.cgi

 

 

 

TABLE 4: Useful tools/approaches for miRNA prediction

Program

Website

Species

miRNAlign

http://bioinfo.au.tsinghua.edu.cn/miralign/

Plant & Animals

MiRFinder

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

Plant & Animals

miREval 2.0

http://mimirna.centenary.org.au/mireval/

Plant & Animals

miRAEST 2.0

http://rhesus.amu.edu.pl/mirnest/copy/

Plant, Animals & Virus

mirExplorer

http://biocenter.sysu.edu.cn/mir/

Plant & Animals

MiRPara

http://www.whiov.ac.cn/bioinformatics/mirpara

Plant & Animals

micro-HARVESTER

http://www-ab.informatik.uni-tuebingen.de/software/microHARVESTER

Plant

MicroPC

http://www3a.biotec.or.th/micropc/

Plant

SplamiR

 http://www.uni-jena.de/SplamiR.html.

Plant

miRTour

http://bio2server.bioinfo.uni-plovdiv.bg/miRTour/

Plant