Main logo
?
tutorial arrow
×
Submit new tools
Share tools covering the current topic. Provide easy-to-follow guidelines to improve their usability.
Share new tools with the community
Sign up for free to promote the availability of bioinformatics tools

MicroRNA target detection software tools | RNA interference

MicroRNAs (miRNA) are short nucleotides that down-regulate its target genes. Various miRNA target prediction algorithms have used sequence complementarity between miRNA and its targets.Source text:(Jung et al., 2015) miRTarVis: an interactive visual…
A A A
TargetScan
Web

TargetScan

Allows prediction of biological targets of miRNAs. With TargetScan user has to…

Allows prediction of biological targets of miRNAs. With TargetScan user has to enter a specie, a human gene symbol, and select either a broadly conserved microRNA family, a conserved microRNA family…

A A A
MIRcheck
Desktop

MIRcheck

Recognizes 20mers with the potential to encode plant miRNAs. MIRcheck can…

Recognizes 20mers with the potential to encode plant miRNAs. MIRcheck can restrict the total number of unpaired nucleotides, the number of bulged or asymmetrically unpaired nucleotides, the number of…

A A A
IntaRNA
Web

IntaRNA

A program for the fast and accurate prediction of interactions between two RNA…

A program for the fast and accurate prediction of interactions between two RNA molecules. It has been designed to predict mRNA target sites for given non-coding RNAs (ncRNAs) like eukaryotic…

A A A
MiRanda
Web

MiRanda

Intends to identify potential microRNA target sites in genomic sequences.…

Intends to identify potential microRNA target sites in genomic sequences. MiRanda provides information about set of genes potentially regulated by a particular microRNA, co-occurrence of predicted…

A A A
TargetScanS
Web

TargetScanS

Search the database of microRNA targets conserved in 5 vertebrates. Conserved…

Search the database of microRNA targets conserved in 5 vertebrates. Conserved targeting was also detected in the open reading frames (ORFs) of vertebrate genomes.

A A A
psRNATarget
Web

psRNATarget

A plant small RNA target analysis server, which features two important analysis…

A plant small RNA target analysis server, which features two important analysis functions: (i) reverse complementary matching between small RNA and target transcript using a proven scoring schema,…

A A A
RNAhybrid
Web

RNAhybrid

A tool for finding the minimum free energy hybridization of a long and a short…

A tool for finding the minimum free energy hybridization of a long and a short RNA. The hybridization is performed in a kind of domain mode, ie. the short sequence is hybridized to the best fitting…

A A A
miSTAR
Web

miSTAR miRNA stacked model target prediction

Uses random forests to model the contribution of individual sites and their…

Uses random forests to model the contribution of individual sites and their genomic context, and logistic regression to combine individual contributions with site count information. miSTAR also…

A A A
miRTar2GO
Dataset

miRTar2GO

A model designed to predict miRNA target sites using more relaxed miRNA-target…

A model designed to predict miRNA target sites using more relaxed miRNA-target binding characteristics. miRTar2GO allows for the prediction of cell-type specific miRNA targets. It was trained on the…

G T A T C G C T A
sRNAtoolbox
Web

sRNAtoolbox

A collection of small RNA analysis tools. sRNAtoolbox is aimed to provide small…

A collection of small RNA analysis tools. sRNAtoolbox is aimed to provide small RNA researchers with several useful tools including sRNA expression profiling from deep sequencing experiments and…

A A A
miRNAMap
Web

miRNAMap

In addition to known miRNA targets, three computational tools previously…

In addition to known miRNA targets, three computational tools previously developed, such as miRanda, RNAhybrid and TargetScan, were applied for identifying miRNA targets in 3' -UTR of genes.…

A A A
TargetScore
Desktop

TargetScore

Infers miRNA targets as the transformed fold-changes weighted by the Bayesian…

Infers miRNA targets as the transformed fold-changes weighted by the Bayesian posteriors given observed target features. Comparing with other methods, targetScore achieves significantly higher…

A A A
RNApredator
Web

RNApredator

A web server for the prediction of sRNA targets. The user can choose from a set…

A web server for the prediction of sRNA targets. The user can choose from a set of over 2155 genomes and plasmids from 1183 bacterial species. RNApredator then uses a dynamic programming approach,…

A A A
ComiR
Web

ComiR Combinatorial miRNA targeting

Predicts whether a given mRNA is targeted by a set of miRNAs. ComiR uses miRNA…

Predicts whether a given mRNA is targeted by a set of miRNAs. ComiR uses miRNA expression to improve and combine multiple miRNA targets for each of the four prediction algorithms: miRanda, PITA,…

A A A
MirAncesTar
Desktop

MirAncesTar

Improves the miRNA target gene (MTG) predictions made with existing tools by…

Improves the miRNA target gene (MTG) predictions made with existing tools by making use of interspecies comparison while taking into account miRNA target binding sites (MTBS) turnover. MirAncesTar…

A A A
TarPmiR
Desktop

TarPmiR Target Prediction for miRNAs

An approach for miRNA target site prediction. TarPmiR applies a…

An approach for miRNA target site prediction. TarPmiR applies a random-forest-based approach to integrate six conventional features and seven new features to predict miRNA target sites. These…

A A A
MiRSEA
Desktop

MiRSEA MicroRNA Set Enrichment Analysis

A computational method to identify the pathways regulated by dysfunctional…

A computational method to identify the pathways regulated by dysfunctional miRNAs. MiRSEA constructs a correlation profile of microRNA and pathways by the hypergeometric statistic test. The gene sets…

A A A
SSCprofiler
Web

SSCprofiler Sequence, Structure and Conservation profiler

A computational tool utilizing a probabilistic method based on Profile Hidden…

A computational tool utilizing a probabilistic method based on Profile Hidden Markov Models to predict novel miRNA precursors. Via the simultaneous integration of biological features such as…

A A A
miRvestigator
Web
Desktop

miRvestigator

Identifies miRNA mediated regulation which is one of several regulators of gene…

Identifies miRNA mediated regulation which is one of several regulators of gene expression including transcription factors (TFs). miRvestigator follows three steps: (1) discovery of co-expressed…

A A A
TargetMiner
Web

TargetMiner

Prediction of microRNA (miRNA) target mRNAs using machine learning approaches…

Prediction of microRNA (miRNA) target mRNAs using machine learning approaches is an important area of research. TargetMiner is a support vector machine (SVM)-based classifier. In addition to…

A A A
miRNet
Web

miRNet

An easy-to-use web-based tool that offers statistical, visual and network-based…

An easy-to-use web-based tool that offers statistical, visual and network-based approaches to help researchers understand miRNAs functions and regulatory mechanisms. The key features of miRNet…

A A A
MiRComb
Desktop

MiRComb

An R package able to combine miRNA and mRNA expression data with hybridization…

An R package able to combine miRNA and mRNA expression data with hybridization information, in order to find potential miRNA-mRNA targets that are more reliable to occur in a specific physiological…

A A A
CCmiR
Desktop

CCmiR Competitive and Cooperative miRNA target prediction

Predicts competitive and cooperative miRNA binding. CCmiR is a hidden Markov…

Predicts competitive and cooperative miRNA binding. CCmiR is a hidden Markov model (HMM) based method that considers the miRNA expression levels and the competition and cooperation of multiple…

A A A
SeedVicious
Desktop

SeedVicious

Predicts microRNA target site. SeedVicious finds microRNA canonical sites plus…

Predicts microRNA target site. SeedVicious finds microRNA canonical sites plus other, less efficient, target sites. It detects near-target sites, which have one nucleotide different from a canonical…

A A A
DIANA-miRPath
Web

DIANA-miRPath

A miRNA pathway analysis web-server, providing accurate statistics, while being…

A miRNA pathway analysis web-server, providing accurate statistics, while being able to accommodate advanced pipelines. mirPath can utilize predicted miRNA targets (in CDS or 3’-UTR regions)…

A A A
myMIR
Dataset

myMIR

Offers a dataset of 3’ -UTR and mature miRNA sequences. myMIR was built…

Offers a dataset of 3’ -UTR and mature miRNA sequences. myMIR was built thanks to a software that permit target identification. This tool overcomes the mere intersection or union of the…

A A A
CopraRNA
Web

CopraRNA Comparative prediction algorithm for small RNA targets

A tool for sRNA target prediction. It computes whole genome predictions by…

A tool for sRNA target prediction. It computes whole genome predictions by combination of distinct whole genome IntaRNA predictions. As input, CopraRNA requires at least 3 homologous sRNA sequences…

A A A
PACCMIT/PACCMIT-CDS
Web

PACCMIT/PACCMIT-CDS Prediction of ACcessible and/or Conserved MIcroRNA Targets

A simple-to-use web server for accurate prediction of targets of both conserved…

A simple-to-use web server for accurate prediction of targets of both conserved and non-conserved miRNAs both in the 3′ UTR (PACCMIT) and in the coding sequences (PACCMIT-CDS). The web server asks…

A A A
MIRZA-G
Desktop

MIRZA-G MIRZA-Genome-wide

A suite of algorithms for the prediction of miRNA targets and siRNA off-targets…

A suite of algorithms for the prediction of miRNA targets and siRNA off-targets on a genome-wide scale. The MIRZA-G variant that uses evolutionary conservation performs better than currently…

A A A
tools4miRs
Web

tools4miRs

A platform that gathers currently more than 160 methods for broadly defined…

A platform that gathers currently more than 160 methods for broadly defined miRNA analysis. The collected tools are classified into several general and more detailed categories in which the users can…

A A A
LncTar
Desktop
Web

LncTar

Explores lncRNA–RNA interactions by finding the minimum free energy joint…

Explores lncRNA–RNA interactions by finding the minimum free energy joint structure of two RNA molecules based on base pairing. LncTar overwhelms the existing RNA–RNA prediction tools on the…

A A A
miRTar
Web

miRTar

An integrated resource for deciphering miRNA-target interaction networks, and…

An integrated resource for deciphering miRNA-target interaction networks, and provides a broad range of analyzing scenarios for miRNA-target interactions, including one miRNA to one gene, one miRNA…

A A A
miRLAB
Desktop

miRLAB

Automates the procedure of inferring and validating miRNA-mRNA regulatory…

Automates the procedure of inferring and validating miRNA-mRNA regulatory relationships. miRLAB provides a complete set of pipelines for testing new methods and analysing new datasets. It includes a…

A A A
TaLasso
Desktop
Web

TaLasso

Quantification of miRNA-mRNA Interactions. The TaLasso web site is an easy tool…

Quantification of miRNA-mRNA Interactions. The TaLasso web site is an easy tool where only few steps are needed to get the interaction scoring results provided by TaLasso algorithm.

A A A
miREvo
Desktop

miREvo

An integrated software platform with a graphical user interface (GUI), to…

An integrated software platform with a graphical user interface (GUI), to process deep-sequencing data of small RNAs and to analyze miRNA sequence and expression evolution based on the…

A A A
miRNAminer
Web

miRNAminer

A web-based tool used for homologous miRNA gene search in several species.…

A web-based tool used for homologous miRNA gene search in several species. Given a search query, candidate homologs are identified using BLAST search and then tested for their known miRNA properties,…

A A A
TargetExpress
Web
Desktop

TargetExpress

Predicts the outcome of overexpression or knockdown experiments across a large…

Predicts the outcome of overexpression or knockdown experiments across a large number of tissues or cell lines. TargetExpress was tested on independent microarray and RNA-Seq experiments of human and…

A A A
targetHub
Web

targetHub

A CouchDB database of miRNA-gene interactions. TargetHub provides a…

A CouchDB database of miRNA-gene interactions. TargetHub provides a programmer-friendly interface to access miRNA targets. The Web site provides RESTful access to miRNA-gene interactions with an…

A A A
HOCTAR
Web

HOCTAR Host gene Opposite Correlated TARgets

A procedure to improve the prediction of miRNA targets. The HOCTAR procedure is…

A procedure to improve the prediction of miRNA targets. The HOCTAR procedure is based on the integration of expression profiling and sequence-based miRNA target recognition softwares. HOCTAR database…

A A A
ToppMiR
Web

ToppMiR

A web-based analytical workbench that allows miRs and mRNAs to be co-analyzed…

A web-based analytical workbench that allows miRs and mRNAs to be co-analyzed via biologically centered approaches in which gene function associated annotations are used to train a machine…

A A A
STarMir
Web

STarMir

Predicts microRNA (miRNA) binding sites on a target ribonucleic acid (RNA).…

Predicts microRNA (miRNA) binding sites on a target ribonucleic acid (RNA). STarMir is an implementation of logistic prediction models developed with miRNA binding data from crosslinking…

A A A
multiMiR
Desktop

multiMiR

A miRNA-target interaction R package and database, which includes several novel…

A miRNA-target interaction R package and database, which includes several novel features not available in existing R packages: (i) compilation of nearly 50 million records in human and mouse from 14…

A A A
metaMIR
Web

metaMIR

Identifies individual miRNAs that co-regulate a subset of the input genes.…

Identifies individual miRNAs that co-regulate a subset of the input genes. metaMIR enables a detailed investigation by identifying miRNAs that target one group while not targeting another group of…

A A A
miRNALasso
Desktop

miRNALasso

A regularized regression approach that is based on the adaptive Lasso procedure…

A regularized regression approach that is based on the adaptive Lasso procedure for detecting functional miRNA-mRNA interactions. miRNALasso fully takes into account the gene sequence features and…

A A A
miRModule
Desktop

miRModule

A software tool for systematic discovery of miRNA modules from a set of…

A software tool for systematic discovery of miRNA modules from a set of predefined miRNA target sites. Given a sets of miRNA binding sites, miRModule efficiently identifies groups of miRNAs, whose…

A A A
comTAR
Web

comTAR COnserved plant MiRNA TARget prediction tool

Allows users to analyze the variations of known miRNA targets during evolution…

Allows users to analyze the variations of known miRNA targets during evolution and to predict previously unknown interactions by focusing on the conservation of the potential targeting. Comtar…

A A A
C-mii
Desktop

C-mii Computational miRNA identification

A software tool specially designed and developed for identifying plant…

A software tool specially designed and developed for identifying plant microRNAs and their targets. C-mii provides following distinguished features. First, it comes with graphical user interfaces of…

A A A
miRNATIP
Desktop

miRNATIP miRNA Target Interaction Predictor

Predicts the miRNA target. miRNATIP is based on a Self-Organizing Map (SOM)…

Predicts the miRNA target. miRNATIP is based on a Self-Organizing Map (SOM) which is trained with the seed region of the miRNA sequences and then the mRNA sequences are projected into the SOM lattice…

G T A T C G C T A
LimiTT
Web

LimiTT

A web-based pipeline which can automatically identify and link validated miRNA…

A web-based pipeline which can automatically identify and link validated miRNA target interactions (MTIs) from extensive lists of miRNAs and target genes in batch mode, even if the provided data is…

A A A
ChemiRs
Web

ChemiRs

Integrates and compares ten miRNA target prediction methods of interest.…

Integrates and compares ten miRNA target prediction methods of interest. ChemiRs provides comprehensive features to facilitate both experimental and computational target predictions. In addition,…

A A A
BCmicrO
Web

BCmicrO

Combines the prediction of different algorithms with Bayesian Network…

Combines the prediction of different algorithms with Bayesian Network (TargetScan, miRanda, PicTar, mirTarget, PITA, and DianamicroT). BCmicrO was evaluated using the training data and the proteomic…

A A A
MirCompare
Web

MirCompare

An algorithm developed to compare sets of microRNAs belonging to different…

An algorithm developed to compare sets of microRNAs belonging to different kingdoms, for their capacity to bind host mRNAs. An efficient double-phase approach based on sequential comparing and…

A A A
DIANA-microT-CD…
Web

DIANA-microT-CDS

A web application dedicated to miRNA target prediction/functional analysis. The…

A web application dedicated to miRNA target prediction/functional analysis. The new DIANA-microT web server aims to further increase the target prediction accuracy and usability of the server…

A A A
Avishkar
Desktop

Avishkar

An efficient SVM-based model for miRNA target prediction utilizing CLIP-seq…

An efficient SVM-based model for miRNA target prediction utilizing CLIP-seq datasets. Avishkar has in its dataset the largest number of potential miRNA-mRNA interaction sets and demonstrates the best…

A A A
miRmap
Desktop
Web

miRmap

Base-pairing of the so-called miRNA “seed” region with mRNAs identifies…

Base-pairing of the so-called miRNA “seed” region with mRNAs identifies many thousands of putative targets. Evaluating the strength of the resulting mRNA repression remains challenging, but is…

A A A
PsRobot
Web

PsRobot

A web-based easy-to-use tool dedicated to the identification of smRNAs with…

A web-based easy-to-use tool dedicated to the identification of smRNAs with stem-loop shaped precursors (such as microRNAs and short hairpin RNAs) and their target genes/transcripts. PsRobot performs…

A A A
microRNA script
Desktop

microRNA script

An integrated genomics and computational analysis to study the potential…

An integrated genomics and computational analysis to study the potential deciding features of transportable microRNAs. Specifically, we analyzed all publicly available microRNAs, a total of 34,612…

A A A
deepTarget
Desktop

deepTarget

Predicts miRNA target. deepTarget is an end-to-end machine learning framework…

Predicts miRNA target. deepTarget is an end-to-end machine learning framework that adopts deep recurrent neural network (RNN)-based auto-encoders to discover the inherent representations of miRNA and…

A A A
anamiR
Desktop

anamiR

Identify potential interactions of miRNA-target gene interactions from miRNA…

Identify potential interactions of miRNA-target gene interactions from miRNA and mRNA expression data. AnamiR contains functions for statistical test, databases of miRNA-target gene interaction and…

A A A
HomoloMTI
Web
Desktop

HomoloMTI Homologous Cluster of MicroRNA Target Interactions

Extents the concept of finding miRNA target sites in conserved sequences among…

Extents the concept of finding miRNA target sites in conserved sequences among multiple orthologous species, integrated three databases, miRTarBase, miRBase and HomoloGene. HomoloMTI reveals the…

A A A
miRTarVis
Desktop

miRTarVis

An interactive visual analysis tool that predicts targets of miRNAs from…

An interactive visual analysis tool that predicts targets of miRNAs from miRNA-mRNA expression profile data and visualizes the resulting miRNA-target interaction network. miRTarVis has intuitive…

A A A
MBSTAR
Desktop
Web

MBSTAR Multiple instance learning of Binding Sites of miRNA TARgets

A machine learning based approach for accurate prediction of true or functional…

A machine learning based approach for accurate prediction of true or functional miRNA binding sites. Multiple instance learning framework is adopted to handle the lack of information about the actual…

A A A
AtmiRNET
Web

AtmiRNET

A resource geared towards plant scientists for reconstructing regulatory…

A resource geared towards plant scientists for reconstructing regulatory networks of Arabidopsis miRNAs. By means of highlighted miRNA studies in target recognition, functional enrichment of target…

A A A
RmiR.Hs.miRNA
Desktop

RmiR.Hs.miRNA

Various databases of microRNA Targets.

Various databases of microRNA Targets.

A A A
miRonTop
Web

miRonTop

Integrates DNA microarrays or high-throughput sequencing data to identify the…

Integrates DNA microarrays or high-throughput sequencing data to identify the potential implication of miRNAs on a specific biological system. miRonTop allows a rapid characterization of the most…

A A A
MiRcode
Web

MiRcode

Provides "whole transcriptome" human microRNA target predictions…

Provides "whole transcriptome" human microRNA target predictions based on the comprehensive GENCODE gene annotation, including >10,000 long non-coding RNA genes. Coding genes are also…

A A A
RNA22
Web

RNA22

A web app for the interactive exploration and in-context visualization of miRNA…

A web app for the interactive exploration and in-context visualization of miRNA target predictions. RNA22 provides an i) informative and comprehensive visualization that is integrated with…

A A A
TAPIR
Web

TAPIR

A web server designed for the prediction of plant microRNA targets. TAPIR…

A web server designed for the prediction of plant microRNA targets. TAPIR offers the possibility to search for plant miRNA targets using a fast and a precise algorithm. The precise option is much…

A A A
CUDA-miRanda
Desktop

CUDA-miRanda

A fast microRNA target identification algorithm that takes advantage of…

A fast microRNA target identification algorithm that takes advantage of massively parallel computing on graphics processing units (GPU) using NVIDIA's compute unified device architecture (CUDA).…

A A A
Antar
Web

Antar

Provides predictions for miRNA targets for human and mouse using two predictive…

Provides predictions for miRNA targets for human and mouse using two predictive models: a model trained from microarray studies following transfection, and a model trained from PAR-CLIP datasets.…

A A A
TargetRank
Web

TargetRank

Scores the seed matches in a UTR relative to a given siRNA or miRNA, and then…

Scores the seed matches in a UTR relative to a given siRNA or miRNA, and then calculates an overall score for the mRNA as a whole by summing the scores for all seed matches present in the 3'…

A A A
p-TAREF
Desktop

p-TAREF plant-TArget REFiner

A machine learning multivariate feature tool has been implemented in parallel…

A machine learning multivariate feature tool has been implemented in parallel and locally installable form, for plant miRNA target identification. p-TAREF refines the process of microRNA target…

A A A
mirTarPri
Web

mirTarPri

A miRNA target prioritization method to rank the predicted target lists from…

A miRNA target prioritization method to rank the predicted target lists from commonly used target prediction methods. Leave-one-out cross validation has proved to be successful in identifying known…

A A A
MultiMiTar
Desktop
Web

MultiMiTar

An efficient miRNA-target prediction system. MultiMiTar is a Support Vector…

An efficient miRNA-target prediction system. MultiMiTar is a Support Vector Machine (SVM) based classifier integrated with a multiobjective metaheuristic based feature selection technique. The robust…

A A A
TargetThermo
Desktop

TargetThermo

Uses an energy-based linear regression model to compute predicted expression…

Uses an energy-based linear regression model to compute predicted expression fold change of a gene caused by a miRNA. TargetThermo does not use conservation in order to allow for predicton of…

A A A
ElMMo
Web

ElMMo

A Bayesian target prediction algorithm without any tunable parameters, that can…

A Bayesian target prediction algorithm without any tunable parameters, that can be applied to sequences from any clade of species. The algorithm automatically infers the phylogenetic distribution of…

A A A
miTarget
Web

miTarget microRNA target prediction

Predicts miRNA target gene. miTarget is a support vector machine (SVM) that…

Predicts miRNA target gene. miTarget is a support vector machine (SVM) that uses a radial basis function kernel as a similarity measure for SVM features, categorized by structural, thermodynamic, and…

A A A
MiRTif
Web

MiRTif MicroRNA:Target Interaction Filter

Provides a miRNA target filtering system. MiRTif is a support vector machine…

Provides a miRNA target filtering system. MiRTif is a support vector machine (SVM) classifier trained with 195 positive and 38 negative miRNA:target interaction pairs, all experimentally validated.…

A A A
Bi-Targeting
Desktop

Bi-Targeting

Identifies groups of viral and host miRNAs that cooperate in…

Identifies groups of viral and host miRNAs that cooperate in post-transcriptional gene regulation, and their target genes that are involved in similar biological processes. Bi-Targeting is an…

A A A
MicroTar
Desktop

MicroTar

A microRNA target prediction program based on mRNA sequence complementarity…

A microRNA target prediction program based on mRNA sequence complementarity (3'-UTR seed matches) and RNA duplex energy prediction, assessing the impact of microRNA binding on complete mRNA…

A A A
SVMicrO
Desktop

SVMicrO

Assumes a 2-stage structure including a site support vector machine (SVM)…

Assumes a 2-stage structure including a site support vector machine (SVM) followed by a UTR-SVM. SVMicrO makes prediction based on 21 optimal site features and 18 optimal UTR features, selected by…

A A A
TargetSpy
Web

TargetSpy

A computational approach for predicting target sites regardless of the presence…

A computational approach for predicting target sites regardless of the presence of a seed match. TargetSpy is based on machine learning and automatic feature selection using a wide spectrum of…

A A A
miREE
Web

miREE

A different approach for miRNA target prediction. miREE is an ensemble of two…

A different approach for miRNA target prediction. miREE is an ensemble of two parts with integrated roles in the prediction an Ab-initio module followed by an SVM module (machine learning technique).

A A A
HomoTarget
Desktop

HomoTarget

Combined pattern recognition neural network (PRNN) and principle component…

Combined pattern recognition neural network (PRNN) and principle component analysis (PCA) architecture has been proposed in order to model the complicated relationship between miRNAs and their target…

A A A
RNASnoop
Desktop

RNASnoop

Predicts complex H/ACA snoRNA–RNA interactions that are outside the scope of…

Predicts complex H/ACA snoRNA–RNA interactions that are outside the scope of conventional RNA–RNA prediction tools. RNAsnoop uses a dynamic programming approach coupled with a nearest-neighbor…

A A A
miRabel
Web

miRabel

Predicts miRNA targets. miRabel can predict mRNAs that are targeted by several…

Predicts miRNA targets. miRabel can predict mRNAs that are targeted by several miRNAs given as input. The experimental expression level of each miRNAs is taken in account to evaluate their potential…

A A A
siRNA Wizard
Web

siRNA Wizard

Helps to select siRNA/shRNA sequences targeting gene(s) of interest. siRNA…

Helps to select siRNA/shRNA sequences targeting gene(s) of interest. siRNA Wizard selects siRNA/shRNA sequences that match criteria suggested by studies of RNA interference and which will have the…

A A A
MAMI
Web

MAMI MetA Mir target Inference

Provides meta predictions of human microRNA targets. MAMI allows searching for…

Provides meta predictions of human microRNA targets. MAMI allows searching for targets of several miRs simultaneously, by separating their identifiers with a new line. It searches by genomic location…

A A A
imiRTP
Desktop

imiRTP

A toolkit to genome-scale identification miRNA-target interactions in…

A toolkit to genome-scale identification miRNA-target interactions in Arabidopsis thaliana. By far, four popular tools (psRNATarget, TAPIR, UEA toolkit, WMD3) and four efficient filters…

A A A
IPA
Desktop

IPA Ingenuity Pathway Analysis

Allows analysis, integration, and interpretation of data derived from omics…

Allows analysis, integration, and interpretation of data derived from omics experiments. IPA is a web-based software application which identifies key regulators and activity to explain expression…

A A A
PicTar
Web

PicTar

An algorithm for the identification of microRNA targets. PicTar miRNA target…

An algorithm for the identification of microRNA targets. PicTar miRNA target site predictions for the human (hg17), mouse (mm7), D. melanogaster (dm2) and C. elegans (ce2) genomes can be obtained…

A A A
mirWIP
Web

mirWIP

Target prediction for animal microRNAs (miRNAs) has been hindered by the small…

Target prediction for animal microRNAs (miRNAs) has been hindered by the small number of verified targets available to evaluate the accuracy of predicted miRNA-target interactions. mirWIP can be used…

G T A T C G C T A
miRGator
Dataset

miRGator

Aims to be the microRNA (miRNA) portal encompassing microRNA diversity,…

Aims to be the microRNA (miRNA) portal encompassing microRNA diversity, expression profiles, target relationships, and various supporting tools. By keeping datasets and analytic tools up-to-date,…

A A A
miTALOS
Web

miTALOS

A web tool that provides insights into miRNA-mediated regulation of biological…

A web tool that provides insights into miRNA-mediated regulation of biological pathways. With the advent of next generation sequencing data resources, miTALOS v2 now incorporates CLIP-seq based miRNA…

A A A
MiMatcher
Desktop

MiMatcher

Performs intragenomic matching followed by classification of miRNA candidates…

Performs intragenomic matching followed by classification of miRNA candidates using support vector machines (SVMs). MiMatcher predicts miRNA candidates and their targets independently in each plant…

A A A
Empirical GO
Desktop

Empirical GO

An algorithm to measure enrichment using an empirical sampling approach, and…

An algorithm to measure enrichment using an empirical sampling approach, and applied this in a reanalysis of the Gene Ontology classes of targets of miRNA lists from 44 published studies. The vast…

A A A
MicroInspector
Web

MicroInspector

A web tool that analyses a user-defined RNA sequence, which is typically an…

A web tool that analyses a user-defined RNA sequence, which is typically an mRNA or a part of an mRNA, for the occurrence of binding sites for known and registered miRNAs. MicroInspector allows…

A A A
mBISON
Web

mBISON miRNA binding site over-representation

Calculates the significance of over-representation of miRNA targets in a given…

Calculates the significance of over-representation of miRNA targets in a given non-ranked gene set. mBISON is based on predictions from TargetScan and uses a randomization step to calculate…

A A A
Raccess
Desktop

Raccess

Computes the accessibility of all the segments of a fixed length for a given…

Computes the accessibility of all the segments of a fixed length for a given RNA sequence when the maximal distance between base pairs is limited to a fixed size W. Raccess is based on an energy…

A A A
NbmiRTar
Web

NbmiRTar

Provides a target prediction method that does not require sequence…

Provides a target prediction method that does not require sequence conservation, using instead, machine learning by a naïve Bayes classifier. NbmiRTar generates a model from sequence and miRNA:mRNA…

A A A
Target-align
Desktop
Web

Target-align

A Smith-Waterman-like alignment tool in order to accurately predict miRNA…

A Smith-Waterman-like alignment tool in order to accurately predict miRNA targets. Dynamic programming was used to build a score matrix based on the complementarity of nucleotides in order to trace…

sigterms
Desktop

sigterms

A desktop software application which retrieves all microRNA:mRNA functional…

A desktop software application which retrieves all microRNA:mRNA functional pairs represented by an experimentally derived set of genes. Sigterms computes, for each microRNA, an enrichment statistic…

A A A
miRTar Hunter
Web

miRTar Hunter

Predicts target sites regardless of the presence or absence of a seed match or…

Predicts target sites regardless of the presence or absence of a seed match or evolutionary sequence conservation. The miRTar Hunter algorithm incorporates sequence-specific features and reflects the…

A A A
miRiam
Desktop

miRiam

A program based on both thermodynamics features and empirical constraints, to…

A program based on both thermodynamics features and empirical constraints, to predict viral miRNAs/human targets interactions. miRiam exploits target mRNA secondary structure accessibility and…

A A A
miRTour
Web

miRTour

Plant miRNA and target prediction tool. miRTour automates all the steps of…

Plant miRNA and target prediction tool. miRTour automates all the steps of miRNA similarity search, miRNA precursor selection, target prediction and annotation, each of them performed with the same…

Information

By using OMICtools you acknowledge that you have read and accepted the terms of the end user license agreement.