Target Prediction

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# Name Description Online/Local Organism
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Algorithm
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References
1 BcmicrO BcmicrO 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 the sensitivity and the specificity of each individual algorithm. /
  • human
  • seed match
  • conservation
  • free energy
  • site accessibility
  • target-site abundance
  • machine learning
  • 3' compensatory pairing
  • G:U pairs allowed in the seed
  • local AU content
  • Bayesian network

  • Homepage

    Publication
    Dec. 17, 2012
    Citations: 6
    2 BioVLAB-MMIA-NGS BioVLAB-MMIA-NGS is Cloud-based miRNA mRNA integraed analysis system using NGS data. System computes differentially/significantly expressed miRNAs (DEmiRNAs) and mRNAs/genes (DEGs), and with targeting information, DEGs targeted by DEmiRNAs and having negative correlation between them are extracted. /
  • human
  • mice
  • macaca
  • plants (rice)
  • seed match
  • conservation
  • free energy
  • site accessibility
  • target-site abundance
  • 3' compensatory pairing
  • G:U pairs allowed in the seed
  • local AU content

  • Homepage

    Publication
    Sept. 29, 2014
    Citations: 5
    3 CleaveLand4 CleaveLand a generalizable computational pipeline for the detection of cleaved miRNA targets from degradome data. CleaveLand takes as input degradome sequences, small RNAs and an mRNA database and outputs small RNA targets. /
  • any
  • seed match
  • conservation
  • free energy
  • G:U pairs allowed in the seed
  • degradome seq analysis

  • Homepage

    Publication
    Nov. 18, 2008
    Citations: 141
    4 ComiR 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. /
  • human
  • mouse
  • worm
  • fly
  • seed match
  • conservation
  • free energy
  • site accessibility
  • target-site abundance
  • machine learning
  • 3' compensatory pairing
  • G:U pairs allowed in the seed
  • local AU content
  • miRNA expression level

  • Homepage

    Publication
    Dec. 20, 2012
    Citations: 15
    5 comTAR comTAR 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. /
  • plants
  • seed match
  • conservation
  • free energy
  • G:U pairs allowed in the seed

  • Homepage

    Publication
    March 14, 2014
    Citations: 2
    6 CPSS CPSS is (a computational platform for the analysis of small RNA deep sequencing data), designed to completely annotate and functionally analyse microRNAs (miRNAs) from NGS data on one platform with a single data submission. /
  • human
  • mouse
  • rat
  • chicken
  • fish
  • other animals (selectable)
  • seed match
  • conservation
  • free energy
  • site accessibility
  • target-site abundance
  • machine learning
  • 3' compensatory pairing
  • G:U pairs allowed in the seed
  • local AU content

  • Homepage

    Publication
    May 9, 2012
    Citations: 18
    7 DeAnnIso DeAnnIso, is an online tool, that is designed for Detection and Annotation of IsomiR from small RNA sequencing data. The detected isomiRs will be classified into different categories. The isomiRs will be aligned with canonical miRNA, and will be annotated with expression, constitution, SNP, and an in-house dataset. It can also extract differentially expressing isomiR between two samples. In addition, IsomiR Bank provides targets prediction and enrichment analysis to evaluate the effects of isomiRs on target selection. /
  • human
  • mouse
  • fish
  • fly
  • plants (selectable)
  • seed match
  • conservation
  • free energy
  • target-site abundance
  • 3' compensatory pairing
  • G:U pairs allowed in the seed

  • Homepage

    Publication
    May 13, 2016
    Citations: 6
    8 DIANA-microT-CDS DIANA-microT-CDS is the 5th version of the microT algorithm. It is specifically trained on a positive and a negative set of miRNA Recognition Elements (MREs) located in both the 3'-UTR and CDS regions. DIANA-microT-CDS provides a significant increase in sensitivity compared to the previous version (65% vs 52%), when compared against experimental proteomics data. /
  • human
  • mouse
  • fly
  • worm
  • seed match
  • conservation
  • free energy
  • site accessibility
  • target-site abundance
  • machine learning
  • 3' compensatory pairing
  • G:U pairs allowed in the seed
  • local AU content

  • Homepage

    Publication
    May 16, 2013
    Citations: 176
    9 ElMMo3 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 posterior probability to each putative target site. /
  • human
  • mouse
  • rat
  • fish
  • fly
  • worm
  • seed match
  • conservation
  • G:U pairs allowed in the seed
  • Bayesian method

  • Homepage

    Publication
    March 1, 2007
    Citations: 135
    10 GUUGle GUUGle efficiently locates potential helical regions under RNA base pairing rules, which include Watson-Crick as well as G-U pairs. It accepts a target and a query set of sequences, and determines all exact matches under RNA rules between target and query sequences that exceed a specified length. /
  • any
  • seed match
  • G:U pairs allowed in the seed

  • Homepage

    Publication
    Jan. 10, 2006
    Citations: 13
    11 homoTarget 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. The results of several types of intelligent classifiers and proposed model were compared, showing that our algorithm outperformed them with higher sensitivity and specificity. Using the recent release of the mirBase database to find potential targets of miRNAs, this model incorporated twelve structural, thermodynamic and positional features of miRNA:mRNA binding sites to select target candidates. /
  • human
  • seed match
  • free energy
  • G:U pairs allowed in the seed
  • local AU content
  • pattern recognition neural network
  • principle component analysis

  • Homepage

    Publication
    Nov. 19, 2012
    Citations: 6
    12 iMir iMir is a modular pipeline for comprehensive analysis of smallRNA-Seq data, comprising specific tools for adapter trimming, quality filtering, differential expression analysis, biological target prediction and other useful options by integrating multiple open source modules and resources in an automated workflow. /
  • any
  • seed match
  • conservation
  • free energy
  • target-site abundance
  • 3' compensatory pairing
  • G:U pairs allowed in the seed
  • local AU content

  • Homepage

    Publication
    Dec. 13, 2013
    Citations: 18
    13 IntaRNA 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. /
  • any
  • seed match
  • free energy
  • site accessibility
  • target-site abundance
  • G:U pairs allowed in the seed

  • Homepage

    Publication
    Oct. 21, 2008
    Citations: 149
    14 isomiR2Function somiR2Function allows for the high-throughput detection of plant isomiRs from any miRNA-seq profiling study. isomiR2Function not only allows for the identification of the templated and non-templated 5′- isomiRs and 3′- isomiRs but also allows for the expression quantification. Since, the prediction of biologically relevant target is an important criterion for the identification of isomiRs and their targets - isomiR2Function identifies target as well. Following target prediction, it allows for functional enrichment of the identified targets. In parallel, isomiR2Function provides support for the visualization of read mapping on corresponding precursor sequences. /
  • plants
  • seed match
  • conservation
  • free energy
  • G:U pairs allowed in the seed
  • degradome seq analysis

  • Homepage

    Publication
    March 21, 2017
    Citations: 0
    15 LeARN/smallA A platform based on LeARN, dedicated to analyse data generated by RNAseq small RNA projects. /
  • any
  • seed match
  • conservation
  • free energy
  • G:U pairs allowed in the seed

  • Homepage

    Publication
    Jan. 14, 2008
    Citations: 8
    16 MAGI MAGI is a web service for fast MicroRNA-Seq data analysis in a graphics processing unit (GPU) infrastructure. Using just a browser, users have access to results as web reports in just a few hours—>600% end-to-end performance improvement over state of the art. /
  • human
  • seed match
  • conservation
  • free energy
  • G:U pairs allowed in the seed

  • Homepage

    Publication
    June 6, 2014
    Citations: 7
    17 MAGIA2 MAGIA2 refines in silico target prediction through miRNA–target expression association measures. MAGIA2 extends the analysis, supporting multiple organisms (human, mouse, rat and drosophila), and using a greatly expanded list of target predictions algorithms. /
  • human
  • mouse
  • rat
  • fly
  • seed match
  • conservation
  • free energy
  • site accessibility
  • target-site abundance
  • machine learning
  • 3' compensatory pairing
  • G:U pairs allowed in the seed
  • local AU content
  • miRNA and gene expression data integration

  • Homepage

    Publication
    May 21, 2012
    Citations: 40
    18 MicroInspector MicroInspector will analyse 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. MicroInspector could spot the correct sites for miRNA-interaction in known target mRNAs. /
  • any (from miRBase)
  • seed match
  • free energy
  • target-site abundance
  • G:U pairs allowed in the seed

  • Homepage

    Publication
    July 1, 2005
    Citations: 87
    19 MicroTar MicroTar is 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. It uses the RNAlib library from the Vienna RNA package /
  • animals
  • seed match
  • free energy
  • site accessibility
  • G:U pairs allowed in the seed

  • Homepage

    Publication
    Dec. 18, 2006
    Citations: 28
    20 miRanda miRanda algorithm is based on a comparisone of miRNAs complementarity to 3'UTR regions. The binding energy of the duplex structure, evolutionary conservation of the whole target site and its position within 3”UTR are calculated and account for a final result which is a weighted soum of match and mismatch scores for base pairs and gap penalties. /
  • any
  • seed match
  • conservation
  • free energy
  • G:U pairs allowed in the seed

  • Homepage

    Publication
    Oct. 5, 2004
    Citations: 1165
    21 miRcode 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 5'UTRs and CDS. Site conservation is evaluated based on 46 vertebrate species. /
  • human
  • seed match
  • conservation

  • Homepage

    Publication
    June 19, 2012
    Citations: 91
    22 miRDB Recently updated features of miRDB, includes 2.1 million predicted gene targets regulated by 6709 miRNAs. In addition to presenting precompiled prediction data, a new feature is the web server interface that allows submission of user-provided sequences for miRNA target prediction. In this way, users have the flexibility to study any custom miRNAs or target genes of interest. /
  • human
  • mouse
  • rat
  • dog
  • chicken
  • seed match
  • conservation
  • free energy
  • site accessibility
  • machine learning
  • 3' compensatory pairing
  • local AU content

  • Homepage

    Publication
    Nov. 5, 2014
    Citations: 204
    23 miRmap To evaluate the strenght of the resulting mRNA repression, the miRNA taregt predictors may employ thermodynamic, evolutionary, probabilistic, or sequence-based features. An open source software library, miRmap, for the first time comprehensively covers all four approaches using eleven predictor features, three of which are novel. Overall, target site accessibility appears to be the most predictive feature. Moreover novel feature based on PhyloP, which evaluates the significance of negative selection, is the best performing predictor in the evolutionary category. /
  • human
  • mouse
  • rat
  • cow
  • chicken
  • zebrafish
  • other animals (selectable)
  • seed match
  • conservation
  • free energy
  • site accessibility
  • local AU content
  • Site over-representation probability

  • Homepage

    Publication
    May 28, 2013
    Citations: 16
    24 miRror Suite The miRror application provides insights on microRNA (miRNA) regulation. It is based on the notion of a combinatorial regulation by an ensemble of miRNAs or genes. miRror integrates predictions from a dozen of miRNA resources that are based on complementary algorithms into a unified statistical framework. For miRNAs set as input, the online tool provides a ranked list of targets, based on set of resources selected by the user, according to their significance of being coordinately regulated. Symmetrically, a set of genes can be used as input to suggest a set of miRNAs. The user can restrict the analysis for the preferred tissue or cell line. /
  • human
  • mouse
  • fly
  • rat
  • worm
  • fish
  • seed match
  • conservation
  • free energy
  • site accessibility
  • target-site abundance
  • machine learning
  • 3' compensatory pairing
  • G:U pairs allowed in the seed
  • local AU content

  • Homepage

    Publication
    June 6, 2014
    Citations: 2
    25 miRTar miRTar, which adopts seven scenarios to identify putative miRNA target sites of the gene transcripts and elucidates the biological functions of miRNAs toward their targets in metabolic pathways. The prediction system cons