TargetScan

Additional Info

  • Activitiy Active
  • Description
    TargetScan predicts biological targets of miRNAs by searching for the presence of conserved 8mer, 7mer, and 6mer sites that match the seed region of each miRNA. As an option, predictions with only poorly conserved sites are also provided. Also identified are sites with mismatches in the seed region that are compensated by conserved 3' pairing and centered sites.
  • Main feature miRNA target prediction
  • Unique features
    Finding broadly conserved, conserved and poorly conserved microRNA families
    Showing miRNA position on gene
    Alignment of miRNA target site in different organisms
  • Organism Human, Mouse, Other vertebrates, Insects, Nematodes, Rat
  • Category Single resource target prediction
  • Last observe Friday, 02 September 2016
  • Year published 2005
  • Citations per year 561.27
  • Last update Wednesday, 01 June 2016
  • Updated over past 3 years Yes
  • Relative Popularity 223704

Bi-Targeting

Additional Info

  • Activitiy Active
  • Description
    "BiTargeting presents a method to identify groups of viral and host miRNAs that cooperate in post-transcriptional gene regulation, and their target genes that are involved in similar biological processes. We call these groups of genes and miRNAs of human and viral origin modules. BiTargeting is demonstrated to be an efficient approach for finding bi-targeting modules of viral and human miRNAs.
  • Main feature Viral and host miRNAs cooperatively regulate host gene expression
  • Unique features
    Viral and host miRNAs that cooperate in gene regulation Integrate miRNA-target binding information, miRNA expression profiles and GO annotations
  • Organism Human
  • Category Single resource target prediction
  • Last observe Wednesday, 31 August 2016
  • Year published 2010
  • Citations per year 2.33
  • Last update Thursday, 13 May 2010
  • Updated over past 3 years No
  • Relative Popularity 41164

DIANA-microT V.4

Additional Info

  • Activitiy Active
  • Description
    DIANA-microT 3.0 provides extensive information for predicted miRNA:target gene interactions providing extensive connectivity to online biological resources. The target prediction algorithm supports parameters calculated individually for each miRNA:target gene interaction and provides a signal-to-noise ratio and a precision score that helps in the evaluation of the significance of the predicted results.
  • Main feature miRNA target prediction
  • Unique features
    Finding targets based on miRNAs, genes or miRNA and gene
    Link to KEGG, UniProt and iHOP
    present predictions of TargetScan or Pictar or verification of TarBase
    Conservation of target sites in different species
  • Organism Human, Mouse
  • Category Single resource target prediction
  • Last observe Wednesday, 31 August 2016
  • Year published 2009
  • Citations per year 44
  • Last update Wednesday, 15 April 2015
  • Updated over past 3 years Yes
  • Relative Popularity 37755

DIANA-microT-CDS V.5

Additional Info

  • Activitiy Active
  • Description
    DIANA-microT v5.0 has been significantly enhanced with an improved target prediction algorithm, DIANA-microT-CDS. microT-CDS is the only algorithm available online, specifically designed to identify miRNA targets both in 3′ untranslated region (3′UTR) and in coding sequences (CDS).
  • Main feature miRNA target prediction
  • Unique features
    Finding targets of a miRNAs based on miRNAs, genes or KEGG descriptions
    Present predictions of TargetScan, Miranda or verification of TarBase
    Conservation of target sites in different species
  • Organism Human, Mouse, Insects, Nematodes
  • Category Single resource target prediction
  • Last observe Friday, 02 September 2016
  • Year published 2013
  • Citations per year 39.66
  • Last update Thursday, 18 April 2013
  • Updated over past 3 years No
  • Relative Popularity 37755

EIMMo

Additional Info

  • Activitiy Inactive
  • Description
    The ElMMo miRNA target prediction method is based on a Bayesian model that only uses comparative genomics information. it has as high an accuracy as other widely used target prediction programs that incorporate additional constraints.
  • Main feature miRNA target prediction
  • Unique features
    Target prediction for mRNAs in subsets of transcripts or different tissue or cell type
    Alignment of multiple genomes in region of predated target site
    Link to smiRNAdb samples that expression of selected miRNA
    is high
  • Organism Human, Mouse, Other vertebrates, Insects, Nematodes, Rat
  • Category Single resource target prediction
  • Last observe Friday, 26 August 2016
  • Year published 2009
  • Citations per year 7.85
  • Last update Thursday, 05 February 2009
  • Updated over past 3 years No
  • Relative Popularity 44014

HomoloMTI

Additional Info

  • Activitiy Active
  • Description
    HomoloMTI constructed to extent the concept of finding miRNA target sites in conserved sequences among multiple orthologous species, integrated three databases, miRTarBase, miRBase and HomoloGene, to reveals the miRNA target interactions might be shared in homologous genes. miRNA target predicts on homologous genes that based on experimental proved microRNA target interaction.
  • Main feature Homology of miRNA target prediction
  • Unique features
    Identifying miRNA target sites on conserved sequences among several species
    Integrated three resources, miRTarBase, miRBase and HomoloGene
  • Organism Human, Mouse, Other vertebrates, Rat
  • Category Single resource target prediction
  • Last observe Friday, 26 August 2016
  • Year published 2011
  • Citations per year 0
  • Last update Friday, 20 May 2011
  • Updated over past 3 years No
  • Relative Popularity 23082

MAMI

Additional Info

  • Activitiy Active
  • Description
    MAMI is a meta mir:target inference for meta prediction of human microRNA targets. Users can tune their desired specificity and sensitivity for target prediction
  • Main feature miRNA target prediction
  • Unique features
    Specificity and sensitivity tuning for prediction
  • Organism Human
  • Category Single resource target prediction
  • Last observe Wednesday, 31 August 2016
  • Year published 2006
  • Citations per year 0
  • Last update Wednesday, 20 December 2006
  • Updated over past 3 years No
  • Relative Popularity 1229

MicroCosm

Additional Info

  • Activitiy Active
  • Description
    A web resource developed by the Enright Lab at the EMBL-EBI containing computationally predicted targets for microRNAs across many species. The miRNA sequences are obtained from the miRBase Sequence database and most genomic sequence from EnsEMBL
  • Main feature miRNA target prediction
  • Unique features
    Microcosm is basically derived from miRBase resource targets
    Search by gene or miRNA name, GO term or keyword
    Alignment of multiple genomes in region of predated target site
  • Organism Human, Mouse, Other vertebrates, Insects, Viruses, Nematodes, Plants
  • Category Single resource target prediction
  • Last observe Wednesday, 31 August 2016
  • Year published 2008
  • Citations per year 309.62
  • Last update Tuesday, 16 October 2007
  • Updated over past 3 years No
  • Relative Popularity 27186

microInspector

Additional Info

  • Activitiy Active
  • Description
    MicroInspector 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. The program allows variation of temperature, the setting of energy values as well as the selection of different miRNA databases to identify miRNA-binding sites of different strength.
  • Main feature miRNA binding sites
  • Unique features
    Finding miRNA binding sites in a target sequence
    Analysis a user-defined RNA sequence
  • Organism Human, Mouse, Other vertebrates, Insects, Viruses, Nematodes, Plants, Rat
  • Category Single resource target prediction
  • Last observe Tuesday, 30 August 2016
  • Year published 2005
  • Citations per year 14.45
  • Last update Wednesday, 27 April 2011
  • Updated over past 3 years No
  • Relative Popularity 286769

microRNA.org

Additional Info

  • Activitiy Active
  • Description
    MicroRNA.org is a comprehensive resource of microRNA target predictions and expression profiles. Target predictions are based on a development of the miRanda algorithm which incorporates current biological knowledge on target rules and on the use of an up-to-date compendium of mammalian microRNAs. A user can explore the set of genes that are potentially regulated by a particular microRNA and the implied cooperativity of multiple microRNAs on a particular mRNA.
  • Main feature miRNA target prediction
  • Unique features
    miRNA target prediction using miRanda algorithm
    Search available for mRNA or miRNA
    Showing miRNA-mRNA interaction
  • Organism Human, Mouse, Insects, Nematodes, Rat
  • Category Single resource target prediction
  • Other covered categories
    miRNA expression
  • Last observe Monday, 29 August 2016
  • Year published 2008
  • Citations per year 122.75
  • Last update Monday, 01 November 2010
  • Updated over past 3 years No
  • Relative Popularity 638003

miRDB

Additional Info

  • Activitiy Active
  • Description
    miRDB is miRNA target prediction and functional annotations database. In this release, web server allows submission of user-provided sequences for miRNA target prediction. Another major update of miRDB is related to functional miRNA annotations. Although thousands of miRNAs have been identified, many of the reported miRNAs are not likely to play active functional roles. To address this issue, we have performed combined computational analyses and literature mining.
  • Main feature miRNA target prediction and functional annotation
  • Unique features
    miRNA target prediction using miRanda algorithm
    Search for multiple miRNAs or genes
  • Organism Human, Mouse, Other vertebrates
  • Category Single resource target prediction
  • Last observe Friday, 26 August 2016
  • Year published 2008
  • Citations per year 48
  • Last update Tuesday, 03 May 2016
  • Updated over past 3 years Yes
  • Relative Popularity 599147

MirEE

Additional Info

  • Activitiy Active
  • Description
    miREE is an ensemble of two parts, the Ab-Initio module to generate a set of candidate sites on the basis of their microRNA-mRNA duplex stability properties and a Support Vector Machine learning module evaluates the impact of microRNA recognition elements on the target gene. As a result, the prediction takes into account information regarding both miRNA-target structural stability and accessibility.
  • Main feature miRNA target prediction
  • Unique features
    miRNA target prediction using an Ab-initio module followed
    by a SVM module
  • Organism Human, Mouse, Nematodes
  • Category Single resource target prediction
  • Last observe Wednesday, 31 August 2016
  • Year published 2011
  • Citations per year 2.8
  • Last update Thursday, 24 November 2011
  • Updated over past 3 years No
  • Relative Popularity 18880

miRMaid

Additional Info

  • Activitiy Active
  • Description
    miRMaid is a software framework, with the goal of integrating miRNA data resources in a uniform web service interface that can be accessed and queried by researchers and by computers. miRMaid is built around data from miRBase and is designed to follow the official miRBase data releases.
  • Main feature Integrating miRNA data sources
  • Unique features
    Integrating miRNA data sources and developing an interface for computer programming
  • Organism Human, Mouse, Other vertebrates, Insects, Viruses, Nematodes, Plants, Rat
  • Category Single resource target prediction
  • Last observe Friday, 02 September 2016
  • Year published 2010
  • Citations per year 1.66
  • Last update Thursday, 14 January 2010
  • Updated over past 3 years No
  • Relative Popularity 26172636

miRNA_Targets

Additional Info

MirTif

Additional Info

  • Activitiy Active
  • Description
    MiRTif (miRNA:target interaction filter) is a machine learning algorithm based on support vector machine that serves as a post-processing filter for the miRNA:target duplexes predicted by softwares such as miRanda, PicTar and TargetScanS. The SVM is trained with validated positive and negative miRNA:target interactions, obtained from TarBase.
  • Main feature miRNA target interaction filter
  • Unique features
    A post-processing filter for the miRNA: gene hybrids prediction of  various algorithms
  • Organism Human, Mouse, Other vertebrates, Insects, Viruses, Nematodes, Plants, Rat
  • Category Single resource target prediction
  • Last observe Friday, 02 September 2016
  • Year published 2008
  • Citations per year 5.375
  • Last update Friday, 12 December 2008
  • Updated over past 3 years No
  • Relative Popularity 89955

Multimitar

Additional Info

  • Activitiy Active
  • Description
    MultiMiTar, a Support Vector Machine based classifier integrated with a multiobjective metaheuristic based feature selection technique. The robust performance of the proposed method is mainly the result of using high quality negative examples and selection of biologically relevant miRNA-targeting site context specific features. True positive predictions are distributed preferentially at the top of the ranked list that makes MultiMiTar reliable for the biologists.
  • Main feature miRNA target prediction
  • Unique features
    Target prediction with multi-objective feature selection
  • Organism Human, Mouse, Other vertebrates, Insects, Viruses, Nematodes, Plants, Rat
  • Category Single resource target prediction
  • Last observe Monday, 29 August 2016
  • Year published 2011
  • Citations per year 4.2
  • Last update Thursday, 15 September 2011
  • Updated over past 3 years No
  • Relative Popularity 122409

NBmiRTar

Additional Info

  • Activitiy Inactive
  • Description
    NBmiRTar does not require sequence conservation, using instead, machine learning by a naïve Bayes classifier. It generates a model from sequence and miRNA:mRNA duplex information from validated targets and artificially generated negative examples. Both the ‘seed’ and ‘out-seed’ segments of the miRNA:mRNA duplex are used for target identification.
  • Main feature miRNA target prediction
  • Unique features
    Target prediction based on NbmiRTar algorithm 
  • Organism Human, Mouse, Other vertebrates, Insects, Viruses, Nematodes, Plants, Rat
  • Category Single resource target prediction
  • Last observe Friday, 26 August 2016
  • Year published 2007
  • Citations per year 9.55
  • Last update Friday, 14 September 2007
  • Updated over past 3 years No
  • Relative Popularity 3356

Patrocles

Additional Info

  • Activitiy Inactive
  • Description
    The Patrocles database compiles DNA sequence polymorphisms that are predicted to perturb miRNA-mediated gene regulation. Distinctive features include: the coverage of seven vertebrate species in its present release, the coverage of the three compartments involved in the silencing, contextual information that enables users to prioritize candidate and a tool (Patrocles finder) that allows the user to determine whether her favorite DSP may perturb miRNA-mediated gene regulation of custom target sequences.
  • Main feature Polymorphisms affect gene regulation
  • Unique features
    DNA polymorphisms predicted to affect miRNA-gene control  
  • Organism Human, Mouse, Other vertebrates, Rat
  • Category Single resource target prediction
  • Last observe Thursday, 01 September 2016
  • Year published 2009
  • Citations per year 12.43
  • Last update Friday, 09 October 2009
  • Updated over past 3 years No
  • Relative Popularity 0

PicTar

Additional Info

  • Activitiy Active
  • Description
    PicTar is a computational method for identifying common targets of microRNAs. Statistical tests using genome-wide alignments of eight vertebrate genomes, PicTar's ability to specifically recover published microRNA targets, and experimental validation of seven predicted targets suggest that PicTar has an excellent success rate in predicting targets for single microRNAs and for combinations of microRNAs.
  • Main feature miRNA target prediction
  • Unique features
    Target prediction based on PicTar algorithm
    Multiple sequence alignment in  region of predated target site 
  • Organism Human, Mouse, Other vertebrates, Insects, Nematodes, Rat
  • Category Single resource target prediction
  • Last observe Sunday, 28 August 2016
  • Year published 2005
  • Citations per year 249
  • Last update Monday, 26 March 2007
  • Updated over past 3 years No
  • Relative Popularity 233214

RepTar

Additional Info

  • Activitiy Active
  • Description
    RepTar is based on identification of repetitive elements in 3'-UTRs and is independent of both evolutionary conservation and conventional binding patterns. The modularity of RepTar enables the prediction of targets with conventional seed sites as well as rarer targets with non-conventional sites, such as sites with seed wobbles, 3'-compensatory sites and the newly discovered centered sites. Furthermore, RepTar's independence of conservation enables the prediction of cellular targets of the less evolutionarily conserved viral miRNAs.
  • Main feature miRNA target prediction
  • Unique features
    Target prediction in human, mouse and several cellular targets of viral miRNAs
  • Organism Human, Mouse
  • Category Single resource target prediction
  • Last observe Thursday, 01 September 2016
  • Year published 2011
  • Citations per year 5.2
  • Last update Wednesday, 01 December 2010
  • Updated over past 3 years No
  • Relative Popularity 29054

STarMir

Additional Info

  • Activitiy Active
  • Description
    STarMir web server predicts microRNA binding sites on a target ribonucleic acid. STarMir is an implementation of logistic prediction models developed with miRNA binding data from crosslinking immunoprecipitation (CLIP) studies. In both intra-dataset and inter-dataset validations, the models showed major improvements over established algorithms in predictions of both seed and seedless sites.
  • Main feature miRNA target prediction
  • Unique features
    Finding miRNA binding sites in a target sequence
    Analysis a user-defined RNA sequence
  • Organism Human, Mouse, Nematodes
  • Category Single resource target prediction
  • Last observe Thursday, 01 September 2016
  • Year published 2004
  • Citations per year 21.25
  • Last update Wednesday, 03 January 2007
  • Updated over past 3 years No
  • Relative Popularity 629399

TargetMiner

Additional Info

  • Activitiy Active
  • Description
    TargetMiner is a support vector machine based classifier which is assessing the prediction accuracy on cross-validation experiments and has been validated with a completely independent experimental test dataset. TargetMiner outperforms 10 existing target prediction algorithms and provides a good balance between sensitivity and specificity that is not reflected in the existing methods.
  • Main feature miRNA target prediction
  • Unique features
    Target prediction with systematic identification of negative examples
  • Organism Human, Mouse, Insects
  • Category Single resource target prediction
  • Last observe Thursday, 01 September 2016
  • Year published 2009
  • Citations per year 13.57
  • Last update Wednesday, 19 August 2009
  • Updated over past 3 years No
  • Relative Popularity 122409

TargetRank

Additional Info

  • Activitiy Active
  • Description
    TargetRank 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 its seed match type, the base composition at position t9, flanking AU content, and flanking conservation.
  • Main feature miRNA target prediction
  • Unique features
    Targeting by endogenous and exogenous microRNAs and siRNAs
  • Organism Human, Mouse
  • Category Single resource target prediction
  • Last observe Wednesday, 31 August 2016
  • Year published 2007
  • Citations per year 22.67
  • Last update Thursday, 13 September 2007
  • Updated over past 3 years No
  • Relative Popularity 756

TargetSpy

Additional Info

  • Activitiy Active
  • Description
    TargetSpy is a novel computational approach for predicting target sites regardless of the presence of a seed match. It is based on machine learning and automatic feature selection using a wide spectrum of compositional, structural, and base pairing features covering current biological knowledge. This model does not rely on evolutionary conservation, which allows the detection of species-specific interactions and makes it suitable for analyzing un conserved genomic sequences.
  • Main feature miRNA target prediction
  • Unique features
    Target prediction based on scores without demanding a seed match
  • Organism Human, Mouse, Other vertebrates, Insects, Rat
  • Category Single resource target prediction
  • Last observe Saturday, 03 September 2016
  • Year published 2010
  • Citations per year 11.5
  • Last update Friday, 01 October 2010
  • Updated over past 3 years No
  • Relative Popularity 12340

ViTa

Additional Info

  • Activitiy Active
  • Description
    ViTa investigate regulatory relationships between host miRNAs and related viruses which curate the known virus miRNA genes and the known/putative target sites of human, mice, rat and chicken miRNAs. ViTa also provides the virus annotations, virus-infected tissues and tissue specificity of host miRNAs. This work also facilitates the comparisons between subtypes of viruses.
  • Main feature miRNA target prediction
  • Unique features
    Prediction of  host miRNA targets in viruses
  • Organism Human, Mouse, Other vertebrates, Viruses, Rat
  • Category Single resource target prediction
  • Last observe Friday, 26 August 2016
  • Year published 2008
  • Citations per year 6
  • Last update Wednesday, 01 February 2006
  • Updated over past 3 years No
  • Relative Popularity 23082

RNAhybrid

Additional Info

  • Activitiy Active
  • Description
    "RNAhybrid is 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 as a means for microRNA target prediction.
  • Main feature Hybridization of two RNA sequence
  • Unique features
    Searching the minimum free energy hybridization of two desired RNA sequences
  • Organism Human, Insects, Nematodes
  • Category User defined sequence target prediction
  • Last observe Thursday, 01 September 2016
  • Year published 2006
  • Citations per year 42
  • Last update Friday, 14 July 2006
  • Updated over past 3 years No
  • Relative Popularity 31617

miRNA_Targets

Additional Info

  • Activitiy Active
  • Description
    miRNA_Targets implemented well establised miRNA target prediction algorithms miRanda and RNAhybrid on mRNA 5 prime UTR's , coding regions and 3 prime UTR's. MicroRNA target predictions using 2 algorithms on 7 genomes. Versatile search capabilities using miRNA or mRNA individually or in groups. Gene ontology classification of sets of target genes. Visualization of miRNA and target gene location network on chromosomes.
  • Main feature Interaction prediction for your own sequence
  • Unique features
    Interaction prediction of a desired sequence and known miRNAs
    Target prediction using miRanda and RNAhybrid  algorithms on
    mRNA 5´ UTR's , coding regions and 3´ UTR's
  • Organism Human, Mouse, Other vertebrates, Insects, Viruses, Nematodes, Plants, Rat
  • Category User defined sequence target prediction
  • Last observe Monday, 29 August 2016
  • Year published 2012
  • Citations per year 3.5
  • Last update Saturday, 25 August 2012
  • Updated over past 3 years No
  • Relative Popularity 15618

PITA

Additional Info

  • Activitiy Active
  • Description
    PITA devise a parameter-free model for microRNA-target interaction that computes the difference between the free energy gained from the formation of the microRNA-target duplex and the energetic cost of unpairing the target to make it accessible to the microRNA. This model explains the variability in our experiments, predicts validated targets more accurately than existing algorithms, and shows that genomes accommodate site accessibility by preferentially positioning targets in highly accessible regions.
  • Main feature Interaction prediction for your own sequence
  • Unique features
    Assessment of interactions between RNA sequences based on PITA algorithm
    Using known miRNAs or user-provided miRNA sequences 
  • Organism Human, Mouse, Insects, Nematodes
  • Category User defined sequence target prediction
  • Last observe Monday, 29 August 2016
  • Year published 2007
  • Citations per year 114.89
  • Last update Sunday, 23 September 2007
  • Updated over past 3 years No
  • Relative Popularity 57269

RNA22 v2

Additional Info

  • Activitiy Active
  • Description
    RNA22, a method for identifying microRNA binding sites and their corresponding heteroduplexes. RNA22 does not rely upon cross-species conservation, is resilient to noise, and, unlike previous methods, it first finds putative microRNA binding sites in the sequence of interest, then identifies the targeting microRNA.
  • Main feature Interaction prediction for your own sequence
  • Unique features
    Identifying microRNA binding sites and their corresponding heteroduplexes
    Interaction prediction between a desired miRNA and target sequence
  • Organism Human, Mouse, Insects, Nematodes
  • Category User defined sequence target prediction
  • Other covered categories
    Single resource target prediction
  • Last observe Thursday, 01 September 2016
  • Year published 2006
  • Citations per year 90.4
  • Last update Thursday, 09 April 2015
  • Updated over past 3 years Yes
  • Relative Popularity 47227

miRWalk 2.0

Additional Info

  • Activitiy Active
  • Description
    miRWalk2.0 is supplying the biggest available collection of predicted and experimentally verified miRNA-target interactions with various novel and unique features. miRWalk2.0 not only documents miRNA binding sites within the complete sequence of a gene, but also combines this information with a comparison of binding sites resulting from 12 existing miRNA-target prediction programs to build novel comparative platforms of binding sites for the promoter, cds, 5’- and 3’-UTR regions. It also documents experimentally verified miRNA-target interaction information collected via an automated text-mining search.
  • Main feature User-friendly composite target prediction resource
  • Unique features
    Combining miRNA target prediction results from DIANA-microT, miRanda, MirTarget2, RNAhybrid, PicTar4,  PicTar5, PITA, RNA22, TargetScan and  miRWalk
    Search of miRNA binding sites within 5´ UTR, CDS and 3´UTR
    Search in all or longer transcripts
    Predicted targets are diagrammed to pathways and diseases
  • Organism Human, Mouse, Rat
  • Category Composite target prediction
  • Other covered categories
    Experimentally validated miRNA targets
    miRNA expression
    miRNA roles in diseases
    miRNA interactions in pathways
  • Last observe Friday, 02 September 2016
  • Year published 2011
  • Citations per year 124.2
  • Last update Tuesday, 21 April 2015
  • Updated over past 3 years Yes
  • Relative Popularity 15843

HocTar

Additional Info

  • Activitiy Active
  • Description
    The HOCTAR (Host gene Opposite Correlated TARgets) tool is a new 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 is the first and unique database to use transcriptomic data to score putative miRNA targets looking at the expression behavior of their host genes, and it includes and re-analyzes all miRNA target predictions generated by softwares such as miRanda, TargetScan and PicTar. The HOCTAR contains the prediction target lists for 290 human intragenic miRNAs and also provides tentative assignments of miRNA function based on Gene Ontology analyses of their predicted targets.
  • Main feature Composite target prediction resource
  • Unique features
    Integrating miRNA target predictions of miRanda, TargetScan and PicTar
  • Organism Human
  • Category Composite target prediction
  • Other covered categories
    Target prediction correlated with expression data
  • Last observe Thursday, 01 September 2016
  • Year published 2011
  • Citations per year 3.8
  • Last update Wednesday, 13 October 2010
  • Updated over past 3 years No
  • Relative Popularity 1410127

mirDIP

Additional Info

  • Activitiy Active
  • Description
    mirDIP integrates prediction databases to elucidate accurate microRNA:target relationships. Pathway-based analysis of mirDIP data suggests microRNAs are involved in intra-pathway signalling. We identify two distinct classes of microRNAs, suggesting a hierarchical organization of microRNAs co-targeting genes both within and between pathways, and implying differential involvement of universe and intra-pathway microRNAs at the disease level.
  • Main feature Composite target prediction source
  • Unique features
    Merging microRNA predictions twelve microRNA prediction datasets  from DIANA-microT, microcosm, miRanda, PicTar, PITA, RNA22 and TargetScan algorithms  
    Finding signaling pathway-associated microRNAS
  • Organism Human
  • Category Composite target prediction
  • Other covered categories
    miRNA interactions in networks
  • Last observe Thursday, 01 September 2016
  • Year published 2011
  • Citations per year 15.4
  • Last update Monday, 01 August 2016
  • Updated over past 3 years Yes
  • Relative Popularity 4704

miRecords

Additional Info

  • Activitiy Active
  • Description
    miRecords is a resource for animal miRNA-target interactions. The Predicted Targets component of miRecords is an integration of predicted miRNA targets produced by 11 established miRNA target prediction programs. The Predicted Targets component of mIRecords integrates the predicted targets of DIANA-microT, MicroInspector, miRanda, MirTarget2, miTarget, NBmiRTar, PicTar, PITA, RNA22, RNAhybrid, and TargetScan/TargertScanS tools.
  • Main feature Composite target prediction source for nine species
  • Unique features
    Combining of predicted miRNA targets produced by 11  algorithms DIANA-microT, MicroInspector, miRanda, MirTarget2, miTarget, NBmiRTar, PicTar, PITA, RNA22, RNAhybrid and TargetScan
    Target predictions can be pooled with the validated interactions
  • Organism Human, Mouse, Other vertebrates, Insects, Nematodes, Rat
  • Category Composite target prediction
  • Other covered categories
    Experimentally validated miRNA targets
  • Last observe Monday, 29 August 2016
  • Year published 2009
  • Citations per year 82.86
  • Last update Saturday, 27 April 2013
  • Updated over past 3 years No
  • Relative Popularity 3131127

MiRGator v3.0

Additional Info

  • Activitiy Active
  • Description
    miRGator aims to be the microRNA (miRNA) portal encompassing microRNA diversity, expression profiles, target relationships, and various supporting tools.miRNA-mRNA target relations and expression correlations integrated for identifying reliable targets. We have merged 3 databases of validated targets and 6 databases of predicted targets. Inverse correlation of gene expression is a strong evidence of genuine targetedness, and we have specifically collected studies with miRNA and mRNA expression data from the same samples.
  • Main feature Composite target prediction source
  • Unique features
    Joining the results of PicTar, TargetScan, miRanda, microcosm, PITA and miRDB algorithms
    Containing microRNA diversity, expression profiles and target relationships
  • Organism Human
  • Category Composite target prediction
  • Other covered categories
    miRNA expression
    miRNA functions
    miRNA interactions in pathways
  • Last observe Friday, 26 August 2016
  • Year published 2013
  • Citations per year 11.3
  • Last update Tuesday, 01 January 2013
  • Updated over past 3 years No
  • Relative Popularity 5075541

miRNA body map

Additional Info

  • Activitiy Active
  • Description
    microRNA body map is an innovative approach to elucidate tissue-specific miRNA functions that goes beyond miRNA target prediction and expression correlation. This approach is based on a multi-level integration of corresponding miRNA and mRNA gene expression levels, miRNA target prediction, transcription factor target prediction and mechanistic models of gene network regulation. Predicted miRNA functions were either validated experimentally or compared to published data.
  • Main feature Composite target prediction resource
  • Unique features
    Integration of predicted miRNA targets produced by eight miRNA target algorithms  PITA, DIANA-microT, Microcosm, RNA22, TargetScan, miRDB, TarBase and mirecords
    miRNA function and their effect on pathways 
  • Organism Human, Mouse, Rat
  • Category Composite target prediction
  • Other covered categories
    miRNA expression
    miRNA function
  • Last observe Wednesday, 31 August 2016
  • Year published 2011
  • Citations per year 6
  • Last update Friday, 22 July 2011
  • Updated over past 3 years No
  • Relative Popularity 17407

miRNAMap 2.0

Additional Info

  • Activitiy Active
  • Description
    miRNAMap 2.0 collect experimental verified microRNAs and experimental verified miRNA target genes in human, mouse, rat, and other metazoan genomes. 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. In order to reduce the false positive prediction of miRNA targets, several criteria are supported for filtering the putative miRNA targets.
  • Main feature Composite target prediction resource
  • Unique features
    Combining miRNA targeting results of Miranda, RNAHybrid and TargetScan algorithms
  • Organism Human
  • Category Composite target prediction
  • Other covered categories
    miRNA expression
  • Last observe Friday, 26 August 2016
  • Year published 2008
  • Citations per year 16.5
  • Last update Sunday, 01 July 2007
  • Updated over past 3 years No
  • Relative Popularity 23082

miRo v 2.0

Additional Info

  • Activitiy Active
  • Description
    miRò is a web-based knowledge base that provides users with miRNA-phenotype associations in humans. It integrates data from various online sources, such as databases of miRNAs, ontologies, diseases and targets, into a unified database equipped with an intuitive and flexible query interface and data mining facilities. The main goal of miRò analysis through sophisticated mining techniques and the introduction of a new layer of associations between genes and phenotypes inferred based on miRNAs annotations.
  • Main feature Composite target prediction resource
  • Unique features
    Integration miRNA target predictions of miRanda, PicTar, TargetScan and mirecords algorithms
  • Organism Human
  • Category Composite target prediction
  • Other covered categories
    miRNA function
    miRNA roles in diseases
  • Last observe Monday, 29 August 2016
  • Year published 2009
  • Citations per year 3.57
  • Last update Tuesday, 23 June 2009
  • Updated over past 3 years No
  • Relative Popularity 46488

mirRor Suite

Additional Info

  • Activitiy Active
  • Description
    miRror-Suite platform developed to yield a robust and concise explanation for miRNA regulation from a large collection of differentially expressed transcripts and miRNAs. Users select the preferred databases from 11 miRNA target prediction resources for predictions and numerous optional filters/parameters that restrict the search to the desired tissues, cell lines, level of expression and predictor scores.
  • Main feature Composite target prediction resource
  • Unique features
    Analyzing series of genes or miRNAs by integrating 11 miRNA target prediction resources
  • Organism Rat
  • Category Composite target prediction
  • Other covered categories
    miRNA interactions in pathways
    miRNA interactions in networks
  • Last observe Thursday, 01 September 2016
  • Year published 2010
  • Citations per year 4.5
  • Last update Wednesday, 23 April 2014
  • Updated over past 3 years Yes
  • Relative Popularity 29054

miRTar

 

 

Additional Info

  • Activitiy Active
  • Description
    MicroRNA Target prediction (miRTar) is 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. It uses RNAHybrid, TargetScan, Miranda and PITA algorithms. It also provides perspective of information on the miRNA targets on alternatively spliced transcripts.
  • Main feature Predicting miRNA targets by integrating RNAhybrid,TargetScan, Miranda and PITA algorithms
  • Unique features
    Finding targets of a miRNAs based on miRNAs, genes or KEGG descriptions
    Present predictions of TargetScan, Miranda or verification of TarBase
    Conservation of target sites in different species
  • Organism Human
  • Category Composite target prediction
  • Other covered categories
    miRNA interactions in pathways
  • Last observe Thursday, 01 September 2016
  • Year published 2011
  • Citations per year 7
  • Last update Tuesday, 26 July 2011
  • Updated over past 3 years Yes
  • Relative Popularity 23092

mimiRNA

Additional Info

Exprtargetdb

Additional Info

  • Activitiy Active
  • Description
    ExprTarget integrate some of the most frequently used miRNA target prediction methods as well as the expression datasets on HapMap cell lines generated in our laboratory. This database conducted an analysis of its performance using the database of experimentally supported miRNA targets as gold standard and using cross-validation. This approach greatly improves miRNA target prediction relative to the existing prediction algorithms.
  • Main feature Correlation of target prediction and expression
  • Unique features
    Integrating Miranda, PicTar and TargetScan miRNA target prediction methods with the mRNA and miRNA expression datasets from HapMap cell lines
  • Organism Human
  • Category Target prediction correlated with expression data
  • Last observe Monday, 29 August 2016
  • Year published 2010
  • Citations per year 6.83
  • Last update Thursday, 21 October 2010
  • Updated over past 3 years No
  • Relative Popularity 1151659

HocTar

Additional Info

  • Activitiy Active
  • Description
    The HOCTAR (Host gene Opposite Correlated TARgets) tool is a new 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 re-analyzes all miRNA target predictions generated by softwares such as miRanda, TargetScan and PicTar.
  • Main feature Correlation of target prediction and expression
  • Unique features
    Integrating Miranda, TargetScan and PicTar predictions with expression results
  • Organism Human
  • Category Target prediction correlated with expression data
  • Other covered categories
    Composite target prediction
  • Last observe Thursday, 01 September 2016
  • Year published 2011
  • Citations per year 3.8
  • Last update Wednesday, 13 October 2010
  • Updated over past 3 years No
  • Relative Popularity 1410127

miRonTop

Additional Info

  • Activitiy Active
  • Description
    MiRonTop is an online tool that integrates DNA microarrays or high-throughput sequencing data to identify the potential implication of miRNAs on a specific biological system. It allows a rapid characterization of the most pertinent mRNA targets according to several existing miRNA target prediction approaches. It usesTargetScan v7.0 and miRTarBase v6.0 algorithms.
  • Main feature Correlation of target prediction and expression
  • Unique features
    Integrating next generation sequencing data and several miRNA target prediction approaches.
  • Organism Human, Mouse, Rat
  • Category Target prediction correlated with expression data
  • Last observe Friday, 26 August 2016
  • Year published 2010
  • Citations per year 5.66
  • Last update Saturday, 01 August 2015
  • Updated over past 3 years Yes
  • Relative Popularity 0

MMIA

Additional Info

  • Activitiy Active
  • Description
    MMIAs is microRNA and mRNA integrated analysis that integrates microRNA and mRNA expression data with predicted microRNA target information for analyzing microRNA-associated phenotypes and biological functions. To assign biological relevance to the integrated microRNA/mRNA profiles, MMIA uses exhaustive human genome coverage, including various disease-associated genes as well as conventional canonical pathways and Gene Ontology.
  • Main feature Correlation of target prediction and expression
  • Unique features
    Combining expression profiles and TargetScan, PicTar and PITA miRNA predictions
  • Organism Human
  • Category Target prediction correlated with expression data
  • Other covered categories
    miRNA roles in diseases
  • Last observe Wednesday, 31 August 2016
  • Year published 2009
  • Citations per year 12.71
  • Last update Tuesday, 14 April 2009
  • Updated over past 3 years No
  • Relative Popularity 0

comTAR

Additional Info

  • Activitiy Active
  • Description

    comTAR is a web tool for the prediction of miRNA targets that is mainly based on the conservation of the potential regulation in different species. The database contains information describing each miRNA-target pair, their function and evolutionary conservation. The tool also allows the search using new miRNAs.

  • Main feature miRNA target prediction
  • Unique features

    Analyze the variations of known miRNA targets during evolution

  • Organism Plants
  • Category Single resource target prediction
  • Last observe Wednesday, 31 August 2016
  • Year published 2014
  • Citations per year 0/5
  • Last update Tuesday, 11 March 2014
  • Updated over past 3 years Yes
  • Relative Popularity 2012608

RNA22 v2

Additional Info

  • Activitiy Active
  • Description
    RNA22, a method for identifying microRNA binding sites and their corresponding heteroduplexes. RNA22 does not rely upon cross-species conservation, is resilient to noise, and, unlike previous methods, it first finds putative microRNA binding sites in the sequence of interest, then identifies the targeting microRNA.
  • Main feature miRNA target prediction
  • Unique features
    Identifying microRNA binding sites and their corresponding heteroduplexes Access pre-computed rna22 target predictions for multiple species
  • Organism Human, Mouse, Insects, Nematodes
  • Category Single resource target prediction
  • Other covered categories
    User defined sequence target prediction
  • Last observe Monday, 29 August 2016
  • Year published 2006
  • Citations per year 90.4
  • Last update Thursday, 09 April 2015
  • Updated over past 3 years Yes
  • Relative Popularity 47207

DIANA-LncBase v2

Additional Info

  • Activitiy Active
  • Description
    LncBase v2 is an extensive collection of miRNA:lncRNA (Long non-coding RNAs ) interactions which includes more than 70 000 direct miRNA:lncRNA experimentally supported interactions, derived from manually curated publications and the analysis of AGO CLIP-Seq libraries. LncBase v2 hosts in silico predicted miRNA targets on lncRNAs, identified with the DIANA-microT algorithm.
  • Main feature miRNA targets on long non-coding RNAs
  • Unique features
    Computationally predicted and experimentally validated results
    Genomic locations
  • Organism Human, Mouse
  • Category Single resource target prediction
  • Last observe Thursday, 01 September 2016
  • Year published 2013
  • Citations per year 27
  • Last update Wednesday, 15 April 2015
  • Updated over past 3 years Yes
  • Relative Popularity 2310477

GUUGle

Additional Info

  • Activitiy Active
  • Description
    GUUGle efficiently locates potential helical regions under RNA base pairing rules, which include Watson–Crick as well as G–U pairs. It accepts a positive and a negative set of sequences, and determines all exact matches under RNA rules between positive and negative sequences that exceed a specified length.
  • Main feature miRNA target prediction
  • Unique features
    Locates potential helical regions under RNA base pairing rules, which include Watson-Crick as well as G-U pairs
  • Organism Human, Mouse, Other vertebrates, Insects, Viruses, Nematodes, Plants, Rat
  • Category Single resource target prediction
  • Last observe Wednesday, 31 August 2016
  • Year published 2006
  • Citations per year 2
  • Last update Thursday, 25 June 2015
  • Updated over past 3 years Yes
  • Relative Popularity 31617

mBISON

Additional Info

  • Activitiy Active
  • Description
    mBISON calculates the significance of over-representation of miRNA targets in a given non-ranked gene set. The gene set can be specified either by a list of genes or by one or more ChIP-seq datasets followed by a user-defined peak-gene association procedure. mBISON is based on predictions from TargetScan and uses a randomization step to calculate False-Discovery-Rates for each miRNA, including a correction for gene set specific properties such as 3'UTR length.
  • Main feature miRNA target prediction
  • Unique features
    Calculates the significance of over-representation of miRNA targets in a given non-ranked gene set
  • Organism Human, Mouse
  • Category Single resource target prediction
  • Last observe Thursday, 01 September 2016
  • Year published 2015
  • Citations per year 0
  • Last update Thursday, 16 April 2015
  • Updated over past 3 years Yes
  • Relative Popularity 233214

miRcode

Additional Info

  • Activitiy Active
  • Description
    miRcode is a comprehensive searchable map of putative microRNA target sites across lncRNA that facilitate the study of microRNA–lncRNA interactions. The miRcode interface provides basic search functionality for finding putative microRNA–target sites in lncRNAs of interest or predicted targets of specific microRNAs.
  • Main feature Whole transcriptome miRNA target prediction
  • Unique features
    Target prediction for mRNA, LncRNA and pseudogene
    Including 5´ UTR's , coding regions and 3´ UTR's
  • Organism Human
  • Category Single resource target prediction
  • Last observe Thursday, 01 September 2016
  • Year published 2012
  • Citations per year 17.75
  • Last update Friday, 01 June 2012
  • Updated over past 3 years No
  • Relative Popularity 3645948

miRmap

Additional Info

  • Activitiy Active
  • Description
    miRmap for the first time comprehensively covers all four approaches of thermodynamic, evolutionary, probabilistic, or sequence-based features using eleven predictor features, three of which are novel. miRmap combined all the features into an integrated model that almost doubles the predictive power of TargetScan.
  • Main feature miRNA target prediction
  • Unique features
    Prediction of microRNA target repression strength
    Including 5´ UTR's , coding regions and 3´ UTR's
  • Organism Human, Mouse, Other vertebrates, Rat
  • Category Single resource target prediction
  • Last observe Thursday, 01 September 2016
  • Year published 2012
  • Citations per year 8.75
  • Last update Wednesday, 09 January 2013
  • Updated over past 3 years No
  • Relative Popularity 5849706

miRNA_Targets

Additional Info

  • Activitiy Active
  • Description
    miRNA_Targets implemented well establised miRNA target prediction algorithms miRanda and RNAhybrid on mRNA 5 prime UTR's , coding regions and 3 prime UTR's. MicroRNA target predictions using 2 algorithms on 7 genomes. Versatile search capabilities using miRNA or mRNA individually or in groups. Gene ontology classification of sets of target genes. Visualization of miRNA and target gene location network on chromosomes.
  • Main feature miRNA target prediction
  • Unique features
    Target prediction using miRanda and RNAhybrid algorithms on mRNA 5´ UTR's , coding regions and 3´ UTR's
  • Organism Other vertebrates, Insects, Nematodes
  • Category Single resource target prediction
  • Last observe Thursday, 01 September 2016
  • Year published 2012
  • Citations per year 3.5
  • Last update Saturday, 25 August 2012
  • Updated over past 3 years No
  • Relative Popularity 15618

MtiBase

Additional Info

  • Activitiy Active
  • Description
    MtiBase (MiRNA-target interactions database) is a database that identify CDS-located and 5'UTR-located miRNA binding sites and systematically evaluate miRNA regulatory effects on mRNA stability and translation by integrating multiple high-throughput experimental datasets such as Ago CLIP-Seq (HITS-CLIP, PAR-CLIP, iCLIP, CLASH), mRNA profiles, ribisome-protected fragment sequencing (RPF) and pulsed stable isotope labeling with amino acids in culture (pSILAC).
  • Main feature miRNA-target interactions database
  • Unique features
    Identify CDS-located and 5'UTR-located miRNA binding sites Systematically evaluate miRNA regulatory effects on mRNA stability and translation
  • Organism Human, Mouse
  • Category Single resource target prediction
  • Last observe Friday, 26 August 2016
  • Year published 2015
  • Citations per year 0
  • Last update Tuesday, 15 September 2015
  • Updated over past 3 years Yes
  • Relative Popularity 14384

P-TAREF

Additional Info

  • Activitiy Active
  • Description
    p-TAREF (plant-Target Refiner) is a Support Vector Regression approach has been implemented for plant miRNA target identification, utilizing position specific dinucleotide density variation information around the target sites, to yield highly reliable result. Performance comparison for p-TAREF was done with other prediction tools for plants with utmost rigor and where p-TAREF was found better performing in several aspects.
  • Main feature miRNA target prediction
  • Unique features
    Refines the process of microRNA target identification through incorporation of local interaction information
  • Organism Plants
  • Category Single resource target prediction
  • Last observe Friday, 26 August 2016
  • Year published 2011
  • Citations per year 2.4
  • Last update Thursday, 29 December 2011
  • Updated over past 3 years No
  • Relative Popularity 472027

TargetRNA2

Additional Info

  • Activitiy Active
  • Description
    TargetRNA2 is a web server that identifies mRNA targets of sRNA regulatory action in bacteria. TargetRNA2 takes the sequence of an sRNA and the name of a sequenced bacterial replicon. TargetRNA2 for searching uses a variety of features, including conservation of the sRNA in other bacteria, the secondary structure of the sRNA, the secondary structure of each candidate mRNA target and the hybridization energy between the sRNA and each candidate.
  • Main feature sRNA target prediction
  • Unique features
    Identifies mRNA targets of sRNA regulatory action in bacteria
  • Organism Bacteria
  • Category Single resource target prediction
  • Last observe Wednesday, 31 August 2016
  • Year published 2014
  • Citations per year 7
  • Last update Tuesday, 01 July 2014
  • Updated over past 3 years Yes
  • Relative Popularity 58178

VIRmiRNA

Additional Info

  • Activitiy Active
  • Description
    VIRmiRNA is the first specialized resource of experimentally proven virus-encoded miRNAs and their associated targets. It includes VIRMIRNA, experimentally validated miRNA sequences with their isomiRs encoded by 44 viruses in viral miRNA, VIRMIRTAR, viral miRNA target genes and AVIRMIR antiviral miRNAs encoded by the host against viruses. This database would enhance the understanding of viral/host gene regulation and may also prove beneficial in the development of antiviral therapeutics.
  • Main feature miRNA target prediction
  • Unique features
    Including VIRmiRNA, VIRmiRtar and AVIRmir subdatabases
    VIRmiRtar contains 7283 target genes of viral miRNAs
    AVIRmir includes 542 antiviral miRNAs encoded by the host against 24 viruses
  • Organism Viruses
  • Category Single resource target prediction
  • Other covered categories
    miRNA sequence and annotation
  • Last observe Monday, 29 August 2016
  • Year published 2008
  • Citations per year 5.375
  • Last update Friday, 07 November 2014
  • Updated over past 3 years Yes
  • Relative Popularity 851615

IntaRNA

Additional Info

  • Activitiy Active
  • Description
    "IntaRNA is 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 can also be used to predict other types of RNA-RNA interactions.
  • Main feature Interaction prediction for your own sequence
  • Unique features
    Prediction of interactions between two RNA molecules
  • Organism Human, Mouse, Other vertebrates, Insects, Viruses, Nematodes, Plants, Rat
  • Category User defined sequence target prediction
  • Last observe Wednesday, 31 August 2016
  • Year published 2008
  • Citations per year 18.75
  • Last update Tuesday, 15 April 2014
  • Updated over past 3 years Yes
  • Relative Popularity 20164

MIRZA

Additional Info

  • Activitiy Active
  • Description
    MIRZA is a biophysical model of miRNA-target interaction and infer its parameters from Argonaute 2 cross-linking and immunoprecipitation data. We show that a substantial fraction of human miRNA target sites are noncanonical and that predicted target-site affinity correlates well with the extent of target destabilization.
  • Main feature Interaction prediction for your own sequence
  • Unique features
    A biophysical miRNA-mRNA interaction model based on Argonaute 2 cross-linking and immunoprecipitation data
  • Organism Human, Mouse, Other vertebrates, Insects, Viruses, Nematodes, Plants, Rat
  • Category User defined sequence target prediction
  • Last observe Monday, 29 August 2016
  • Year published 2013
  • Citations per year 16.67
  • Last update Sunday, 20 January 2013
  • Updated over past 3 years No
  • Relative Popularity 44014

MR-microT

Additional Info

  • Activitiy Active
  • Description
    MR-microT is a MapReduce-based implementation of microT target prediction method. It provides near-real time predictions for custom miRNA sequences. MR-microT offers the highly requested by life scientists feature of predicting the targets of ad-hoc miRNA molecules in near-real time through an intuitive Web interface.
  • Main feature Interaction prediction for your own sequence
  • Unique features
    Provides near-real time predictions for custom miRNA sequences
  • Organism Human, Mouse, Insects
  • Category User defined sequence target prediction
  • Last observe Friday, 26 August 2016
  • Year published 2012
  • Citations per year 25.25
  • Last update Monday, 30 June 2014
  • Updated over past 3 years Yes
  • Relative Popularity 579395

psRNATarget

Additional Info

  • Activitiy Active
  • Description
    psRNATarget, a plant small RNA target analysis server, which features two important analysis functions: reverse complementary matching between miRNA and target transcript using a proven scoring schema, and target site accessibility evaluation by calculating unpaired energy required to open secondary structure around miRNA’s target site on mRNA. PsRNATarget distinguishes translational and post-transcriptional inhibition, and it reports the number of miRNA/target site pairs that may affect miRNA binding activity to target transcript
  • Main feature miRNA target prediction
  • Unique features
    Reverse complementary matching between miRNA and target transcript using a proven scoring schema Target site accessibility evaluation by calculating unpaired energy
  • Organism Plants
  • Category User defined sequence target prediction
  • Last observe Friday, 02 September 2016
  • Year published 2011
  • Citations per year 90.4
  • Last update Friday, 01 July 2011
  • Updated over past 3 years No
  • Relative Popularity 335799

TAPIR

Additional Info

  • Activitiy Active
  • Description
    TAPIR is designed for the prediction of plant microRNA targets. The server 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 miRNA-target duplexes. Furthermore, the precise option allows the prediction of target mimics, which are characterized by a miRNA-target duplex having a large loop, making them undetectable by traditional tools.
  • Main feature miRNA target prediction
  • Unique features
    Search for plant miRNA targets using a fast and a precise algorithm User defined score and free energy ratio
  • Organism Plants
  • Category User defined sequence target prediction
  • Last observe Wednesday, 31 August 2016
  • Year published 2010
  • Citations per year 10
  • Last update Thursday, 29 April 2010
  • Updated over past 3 years Yes
  • Relative Popularity 17611

BcmicrO

Additional Info

  • Activitiy Active
  • Description
    Since different existing algorithms rely on different features and classifiers, there is a poor agreement among the results of different algorithms. To benefit from the advantages of different algorithms, we proposed an algorithm called BCmicrO that combines the prediction of TargetScan, miRanda, PicTar, mirTarget, PITA, and DianamicroT.
  • Main feature Composite target prediction resource
  • Unique features
    Combines the prediction of TargetScan, miRanda, PicTar, mirTarget, PITA, and Diana microT
  • Organism Human
  • Category Composite target prediction
  • Last observe Monday, 29 August 2016
  • Year published 2012
  • Citations per year 0.25
  • Last update Monday, 17 December 2012
  • Updated over past 3 years No
  • Relative Popularity 26378

26378

Additional Info

  • Activitiy Active
  • Description
    ComiR (Combinatorial miRNA targeting) 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 four algorithms are then combined using a support vector machine trained on Drosophila Ago1 IP data.
  • Main feature Composite target prediction resource
  • Unique features
    Combining miRNA target prediction results from miRanda, PITA, TargetScan and mirSVR Using miRNA expression to improve and combine multiple miRNA targets
  • Organism Human, Mouse, Insects, Nematodes
  • Category Composite target prediction
  • Last observe Monday, 29 August 2016
  • Year published 2013
  • Citations per year 16.67
  • Last update Tuesday, 20 October 2015
  • Updated over past 3 years Yes
  • Relative Popularity 7995

miRGate

Additional Info

  • Activitiy Active
  • Description
    miRGate is a curated database of human, mouse and rat miRNAs/mRNAs targets. It is designed to analyze miRNA and gene isoforms lists under a common and consistent space of annotations. Including all existing 3 UTR and the entirely known miRNAs. All Havana biotypes and ENCODE principal isoforms for the three organisms are also included.
  • Main feature Composite target prediction resource
  • Unique features
    Using miRanda, Pita, RNAHybrid, Microtar, TargetScan, TarBase, mirTarBase and miRecords
    Analyze miRNA and gene isoforms lists under a common and consistent space of annotations
  • Organism Human, Mouse, Rat
  • Category Composite target prediction
  • Last observe Monday, 29 August 2016
  • Year published 2015
  • Citations per year 4
  • Last update Friday, 20 March 2015
  • Updated over past 3 years Yes
  • Relative Popularity 682038

miRSystem

Additional Info

  • Activitiy Active
  • Description
    miRSystem is a database which integrates seven well known miRNA target gene prediction programs: DIANA,miRanda, miRBridge, PicTar, PITA, rna22and TargetScan. This database contains validated data from TarBase and miRecords on interaction between miRNA and its target genes.
  • Main feature Composite target prediction resource
  • Unique features
    Combining miRNA targeting of DIANA, miRanda, miRBridge, PicTar, PITA, rna22 and TargetScan algorithms
  • Organism Human, Mouse
  • Category Composite target prediction
  • Last observe Wednesday, 31 August 2016
  • Year published 2012
  • Citations per year 11.5
  • Last update Friday, 13 May 2016
  • Updated over past 3 years Yes
  • Relative Popularity 6285

mirTarPri

Additional Info

  • Activitiy Active
  • Description
    mirTarPri is a web toolkit for prioritising candidate mirRNA targets in the context of functional genomic data. mirTarPri also provides a full prioritized mirRNA target list of six commonly used methods TargetScan, PicTar, PITA, DIANA-microT, miRanda and RNAhybrid
  • Main feature Composite target prediction based on functional genomic data
  • Unique features
    Prioritizing candidate mirRNA targets in the context of functional genomic data
    Using Gene Ontology and protein protein interaction networks
    Provides mirRNA target list of TargetScan, PicTar, PITA,DIANA-microT, miRanda, RNAhybrid tarBase, mirRecord and mir2Disease
  • Organism Human
  • Category Composite target prediction
  • Last observe Friday, 02 September 2016
  • Year published 2013
  • Citations per year 1.33
  • Last update Wednesday, 09 January 2013
  • Updated over past 3 years No
  • Relative Popularity 0

multiMiR

Additional Info

  • Activitiy Active
  • Description
    multiMiR is a comprehensive collection of predicted and validated miRNA-target interactions and their associations with diseases and drugs. multiMiR collecting nearly 50 million records from 14 different databases. User-defined cutoffs for predicted binding strength to provide the most confident selection.
  • Main feature Composite target prediction resource
  • Unique features
    Using predicted and validate miRNA-target Interactions
    Using DIANA-microT-CDS, ElMMo, MicroCosm, miRanda, miRDB, PicTar, PITA, TargetScan, miRecords, miRTarBase and TarBase algorithms
  • Organism Human, Mouse
  • Category Composite target prediction
  • Last observe Friday, 02 September 2016
  • Year published 2014
  • Citations per year 4.5
  • Last update Thursday, 24 July 2014
  • Updated over past 3 years Yes
  • Relative Popularity 19884

targetHub

Additional Info

  • Activitiy Active
  • Description
    targetHub is a database of miRNA-mRNA interactions. The interaction data is obtained various external data sources and in some cases computed in-house by algorithms implemented for miRNA target prediction
  • Main feature Composite target prediction resource
  • Unique features
    Using predicted and validate miRNA-target Interactions
    Using miRanda, PicTar4, PicTar5, TargetScan, miRecords and miRTarBase algorithms
  • Organism Human
  • Category Composite target prediction
  • Last observe Friday, 26 August 2016
  • Year published 2013
  • Citations per year 0.33
  • Last update Thursday, 29 August 2013
  • Updated over past 3 years No
  • Relative Popularity 28897

ToppMiR

Additional Info

  • Activitiy Active
  • Description
    ToppMiR is 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 biological contexts based on gene associated information from expression data or from a user-specified set of genes that relate to context-relevant knowledge or hypotheses.
  • Main feature Composite target prediction and ranking
  • Unique features
    Ranking targets based on biological functions and context
    Using PicTar, mirSVR, TargetScan, MSigDB, PITA, miRecords and miRTarbase algorithms
  • Organism Human
  • Category Composite target prediction
  • Last observe Saturday, 03 September 2016
  • Year published 2014
  • Citations per year 2.5
  • Last update Monday, 28 April 2014
  • Updated over past 3 years Yes
  • Relative Popularity 122953

TaLasso

Additional Info

  • Activitiy Active
  • Description
    TaLasso was used on two public datasets that have paired expression levels of human miRNAs and mRNAs. The top ranked interactions recovered by TaLasso are especially enriched (more than using any other algorithm) in experimentally validated targets. The functions of the genes with mRNA transcripts in the top-ranked interactions are meaningful.
  • Main feature Human Correlation of mRNA and miRNA expression
  • Unique features
    Combines the information of sequence databases with mRNA and miRNA expression to quantify the down-regulation between miRNAs and their putative targets
  • Organism Human
  • Category Target prediction correlated with expression data
  • Last observe Monday, 29 August 2016
  • Year published 2012
  • Citations per year 6.25
  • Last update Tuesday, 14 February 2012
  • Updated over past 3 years No
  • Relative Popularity 24948