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.
AtmiRNET
AtmiRNET
A resource geared towards plant scientists for reconstructing regulatory networks of…
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 genes, promoter identification, and detection of…
Avishkar
Avishkar
An efficient SVM-based model for miRNA target prediction utilizing CLIP-seq datasets.…
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 performance among other established computational…
BCmicrO
BCmicrO
Combines the prediction of different algorithms with Bayesian Network (TargetScan,…
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 data. The results show that BCmicrO improves both…
Combinatorial miRNA targeting
Combinatorial miRNA targeting
ComiR
Predicts whether a given mRNA is targeted by a set of miRNAs. ComiR uses miRNA expression…
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, TargetScan and mirSVR. The composite scores of the…
Comparative prediction algorithm for small RNA…
Comparative prediction algorithm for small RNA targets
CopraRNA
A tool for sRNA target prediction. It computes whole genome predictions by combination of…
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 from 3 distinct organisms in FASTA format. The…
Computational miRNA identification
Computational miRNA identification
C-mii
A software tool specially designed and developed for identifying plant microRNAs and…
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 well-defined pipelines for both miRNA and target…
COnserved plant MiRNA TARget prediction tool
COnserved plant MiRNA TARget prediction tool
comTAR
Allows users to analyze the variations of known miRNA targets during evolution and to…
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 contains precomputed data for 22 conserved miRNAs where…
CUDA-miRanda
CUDA-miRanda
A fast microRNA target identification algorithm that takes advantage of massively…
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). CUDA-miRanda specifically focuses on the local…
DIANA-microT-CDS
DIANA-microT-CDS
A web application dedicated to miRNA target prediction/functional analysis. The new…
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 interface, while facilitating users aiming to perform…
DIANA-miRPath
DIANA-miRPath
A miRNA pathway analysis web-server, providing accurate statistics, while being able to…
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) provided by the DIANA-microT-CDS algorithm or even…
ElMMo
ElMMo
A Bayesian target prediction algorithm without any tunable parameters, that can be…
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 functional sites for each miRNA, and assigns a…
Empirical GO
Empirical GO
An algorithm to measure enrichment using an empirical sampling approach, and applied this…
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 majority of the miRNA target sets were not…
HomoTarget
HomoTarget
Combined pattern recognition neural network (PRNN) and principle component analysis (PCA)…
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 mRNAs in humans. Using the recent release of the…
Host gene Opposite Correlated TARgets
Host gene Opposite Correlated TARgets
HOCTAR
A procedure to improve the prediction of miRNA targets. The HOCTAR procedure is based on…
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 (db) is the first and unique database to use…
imiRTP
imiRTP
A toolkit to genome-scale identification miRNA-target interactions in Arabidopsis…
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 (multi-method, multiplicity, accessibility and Degradome-seq…
IntaRNA
IntaRNA
A program for the fast and accurate prediction of interactions between two RNA molecules.…
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 microRNAs (miRNAs) or bacterial small RNAs (sRNAs), but it…
IPA (MicroRNA Research)
IPA (MicroRNA Research)
Reduces the number of steps it takes to confidently, quickly, and easily identify mRNA…
Reduces the number of steps it takes to confidently, quickly, and easily identify mRNA targets. The microRNA capabilities in IPA provide insights into the biological effects of microRNAs, using experimentally validated interactions from TarBase,…
LncTar
LncTar
Shows the ability to efficiently predict the RNA targets of lncRNAs in a large scale.…
Shows the ability to efficiently predict the RNA targets of lncRNAs in a large scale. LncTar is an efficient tool for the fast identification of the RNA targets of lncRNAs. LncTar does not have limit to RNA size, indicating LncTar can be used to all…
MicroInspector
MicroInspector
A web tool that analyses a user-defined RNA sequence, which is typically an mRNA or a…
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 variation of temperature, the setting of energy values…
MicroTar
MicroTar
A microRNA target prediction program based on mRNA sequence complementarity (3'-UTR…
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 molecules. MicroTar uses the RNAlib library from the…
MiRcode
MiRcode
Provides "whole transcriptome" human microRNA target predictions based on the…
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 covered, including atypical regions such as…
MiRdup
MiRdup
A computational predictor for the identification of the most likely miRNA location within…
A computational predictor for the identification of the most likely miRNA location within a given pre-miRNA or the validation of a candidate miRNA. MiRdup is based on a random forest classifier trained with experimentally validated miRNAs from…
miREE
miREE
A different approach for miRNA target prediction. miREE is an ensemble of two parts with…
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).
miREvo
miREvo
An integrated software platform with a graphical user interface (GUI), to process…
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 multiple-species whole genome alignments (WGAs). Three major…
miRGator
miRGator
Aims to be the microRNA (miRNA) portal encompassing microRNA diversity, expression…
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, miRGator should continue to serve as an integrated…
miRiam
miRiam
A program based on both thermodynamics features and empirical constraints, to predict…
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 interaction rules, inferred from validated miRNA/mRNA…
miRmap
miRmap
Base-pairing of the so-called miRNA “seed” region with mRNAs identifies many…
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 essential for a biologically informative ranking of…
miRModule
miRModule
A software tool for systematic discovery of miRNA modules from a set of predefined miRNA…
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 binding sites significantly co-occur in the same set…
miRNALasso
miRNALasso
A regularized regression approach that is based on the adaptive Lasso procedure for…
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 the miRNA and mRNA expression profiles. Given a set…
miRNAMap
miRNAMap
In addition to known miRNA targets, three computational tools previously developed, such…
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. Various criteria for filtering the putative miRNA…
miRNAminer
miRNAminer
A web-based tool used for homologous miRNA gene search in several species. Given a search…
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, such as secondary structure, energy, alignment…
miRTar
miRTar
A tool that enables biologists easily to identify the biological functions and regulatory…
A tool that enables biologists easily to identify the biological functions and regulatory relationships between a group of known/putative miRNAs and protein coding genes. miRTar also provides perspective of information on the miRNA targets on…
mirTarPri
mirTarPri
A miRNA target prioritization method to rank the predicted target lists from commonly…
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 targets, achieving an AUC score up to 0. 84.…
miRTarVis
miRTarVis
An interactive visual analysis tool that predicts targets of miRNAs from miRNA-mRNA…
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 interface design in accordance with the analysis…
miRTour
miRTour
Plant miRNA and target prediction tool. miRTour automates all the steps of miRNA…
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 set of input sequences.
mirWIP
mirWIP
Target prediction for animal microRNAs (miRNAs) has been hindered by the small number of…
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 to capture all known conserved miRNA-mRNA target…
MIRZA-Genome-wide
MIRZA-Genome-wide
MIRZA-G
A suite of algorithms for the prediction of miRNA targets and siRNA off-targets on a…
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 available methods in predicting canonical miRNA target…
multiMiR
multiMiR
A miRNA-target interaction R package and database, which includes several novel features…
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 different databases, more than any other…
MultiMiTar
MultiMiTar
An efficient miRNA-target prediction system. MultiMiTar is a Support Vector Machine…
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 performance of the proposed method is mainly the…
Multiple instance learning of Binding Sites of…
Multiple instance learning of Binding Sites of miRNA TARgets
MBSTAR
A machine learning based approach for accurate prediction of true or functional miRNA…
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 binding sites in the target mRNAs.
PicTar
PicTar
An algorithm for the identification of microRNA targets. PicTar miRNA target site…
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 from the UCSC Genome browser via the…
plant-TArget REFiner
plant-TArget REFiner
p-TAREF
A machine learning multivariate feature tool has been implemented in parallel and locally…
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 identification through incorporation of local…
Prediction of ACcessible and/or Conserved…
Prediction of ACcessible and/or Conserved MIcroRNA Targets
PACCMIT/PACCMIT-CDS
A simple-to-use web server for accurate prediction of targets of both conserved and…
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 the user for microRNAs and mRNAs to be analyzed,…
psRNATarget
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, and (ii) target-site accessibility evaluation by…
PsRobot
PsRobot
A web-based easy-to-use tool dedicated to the identification of smRNAs with stem-loop…
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 fast analysis to identify smRNAs with stem-loop…
RmiR.Hs.miRNA
RmiR.Hs.miRNA
Various databases of microRNA Targets.
Various databases of microRNA Targets.
RNA22
RNA22
A pattern-based algorithm for the discovery of microRNA target sites and the…
A pattern-based algorithm for the discovery of microRNA target sites and the corresponding heteroduplexes. RNA22-GUI is currently available for Homo sapiens, Mus musculus, Drosophila melanogaster and Caenorhabditis elegans.
RNAhybrid
RNAhybrid
A tool for finding the minimum free energy hybridization of a long and a short RNA. The…
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 part of the long one. The tool is primarily meant…
RNApredator
RNApredator
A web server for the prediction of sRNA targets. The user can choose from a set of over…
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, RNAplex, to compute putative targets. Compared to…
Sequence, Structure and Conservation profiler
Sequence, Structure and Conservation profiler
SSCprofiler
A computational tool utilizing a probabilistic method based on Profile Hidden Markov…
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 sequence, structure and conservation, SSCprofiler achieves…
sRNAtoolbox
sRNAtoolbox
A collection of small RNA analysis tools. sRNAtoolbox is aimed to provide small RNA…
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 several downstream analysis tools. The center piece of…
STarMir
STarMir
Predicts microRNA (miRNA) binding sites on a target ribonucleic acid (RNA). STarMir is an…
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 immunoprecipitation (CLIP) studies. The input data for STarMir…
SVMicrO
SVMicrO
Assumes a 2-stage structure including a site support vector machine (SVM) followed by a…
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 training from a comprehensive collection of 113 site…
TaLasso
TaLasso
Quantification of miRNA-mRNA Interactions. The TaLasso web site is an easy tool where…
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.
TAPIR
TAPIR
A web server designed for the prediction of plant microRNA targets. TAPIR offers the…
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 slower but guarantees to find less perfectly paired…
Target-align
Target-align
A Smith-Waterman-like alignment tool in order to accurately predict miRNA targets.…
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 the optimal local alignments. Compared to other…
targetHub
targetHub
A CouchDB database of miRNA-gene interactions. TargetHub provides a programmer-friendly…
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 assortment of gene and miRNA identifiers. It can be a…
TargetMiner
TargetMiner
Prediction of microRNA (miRNA) target mRNAs using machine learning approaches is an…
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 assessing the prediction accuracy on cross-validation…
TargetRank
TargetRank
Scores the seed matches in a UTR relative to a given siRNA or miRNA, and then calculates…
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' UTR. The score for each seed match is based on (1)…
TargetScan
TargetScan
Predicts biological targets of miRNAs by searching for the presence of conserved 8mer and…
Predicts biological targets of miRNAs by searching for the presence of conserved 8mer and 7mer sites that match the seed region of each miRNA. As an option, nonconserved sites are also predicted. Also identified are sites with mismatches in the seed…
TargetScanS
TargetScanS
Search the database of microRNA targets conserved in 5 vertebrates. Conserved targeting…
Search the database of microRNA targets conserved in 5 vertebrates. Conserved targeting was also detected in the open reading frames (ORFs) of vertebrate genomes.
TargetScore
TargetScore
Infers miRNA targets as the transformed fold-changes weighted by the Bayesian posteriors…
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 accuracy in identifying known targets in most tests.…
TargetSpy
TargetSpy
A computational approach for predicting target sites regardless of the presence of a seed…
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 compositional, structural, and base pairing features…
TargetThermo
TargetThermo
Uses an energy-based linear regression model to compute predicted expression fold change…
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 non-conserved targets. First, the program searches for…
ToppMiR
ToppMiR
A web-based analytical workbench that allows miRs and mRNAs to be co-analyzed via…
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 learning-based analysis engine. ToppMiR learns about…