Target Prediction

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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: 6
    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: 148
    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: 3
    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: 7
    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: 194
    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: 141
    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: 14
    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: 20
    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: 156
    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: 8
    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: 42
    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: 29
    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: 1187
    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: 103
    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: 237
    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: 20
    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 considers seven scenarios (one miRNA to one gene, one miRNA to N genes, N miRNAs to one gene, N miRNAs to M genes, all miRNAs to N genes and N miRNAs to metabolic pathways) to help biologists to identify easily the regulatory relationships between interesting miRNAs and their targets, not only in 3'UTR but also in 5'UTR and coding regions. /
  • human
  • seed match
  • conservation
  • free energy
  • site accessibility
  • target-site abundance
  • 3' compensatory pairing
  • G:U pairs allowed in the seed
  • local AU content
  • alternative splicing analysis

  • Homepage

    Publication
    July 26, 2011
    Citations: 35
    26 miRTarCLIP From miRTarCLIP scratch, it automatically removes adaptor sequences from raw reads, filters low quality reads, reverts C to T, aligns reads to 3'UTRs, scans for read clusters, identifies high confidence miRNA target sites, and provides annotations from external databases. With multi-threading techniques and our novel C to T reversion procedure, miRTarCLIP greatly reduces the running time comparing to conventional approaches. /
  • human
  • mouse
  • seed match
  • conservation
  • free energy
  • target-site abundance
  • 3' compensatory pairing
  • G:U pairs allowed in the seed
  • local AU content
  • CLIP seq analysis

  • Homepage

    Publication
    Jan. 21, 2013
    Citations: 18
    27 mirTools 2.0 MirTools 2.0 is updated version of mirTools, which was developed to comprehensive characterize the small RNA transcriptome obtained from high-throughput sequencing. It enables user to: detect and profile non-coding RNA (tRNA, snRNA, snoRNA, rRNA ans piRNA); obtain detailed annotation ifmromation about known miRNA (absolute/realtive reds count and most abundant tags); identify the microRNA targeted genes and their detailed functional annotate; perform the comparison of many samples and identify the differentially expressed non-coding RNAs between experimental groups; discovery the novel miRNAs. /
  • human
  • mouse
  • rat
  • chicken
  • fish
  • worm
  • fly
  • other animals (selectable)
  • plants (selectable)
  • any (local)
  • seed match
  • conservation
  • free energy
  • site accessibility
  • machine learning
  • 3' compensatory pairing
  • G:U pairs allowed in the seed
  • local AU content

  • Homepage

    Publication
    May 29, 2013
    Citations: 28
    28 mirWIP mirWIP can be used to capture all known conserved miRNA-mRNA target relationships in Caenorhabditis elegans at a lower false-positive rate than can the current standard methods /
  • Worm
  • seed match
  • conservation
  • free energy
  • site accessibility
  • target-site abundance
  • G:U pairs allowed in the seed

  • Homepage

    Publication
    Aug. 17, 2008
    Citations: 98
    29 MIRZA A rigorous biophysical model of miRNA-target interaction and infer its energy parameters from Ago-CLIP data. The model includes parameters associated with base pairs and loops and specific miRNA position–dependent energy parameters that reflect the constraints imposed by the Argonaute protein on miRNA-mRNA interaction. /
  • human
  • seed match
  • free energy
  • 3' compensatory pairing
  • G:U pairs allowed in the seed
  • miRNA expression (needed)

  • Homepage

    Publication
    Jan. 20, 2013
    Citations: 54
    30 MIRZA-G 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 sites and in addition, it predicts non-canonical miRNA target sites with similarly high accuracy. Furthermore, MIRZA-G variants predict siRNA off-target sites with an accuracy unmatched by currently available programs. /
  • human
  • seed match
  • conservation
  • free energy
  • site accessibility
  • 3' compensatory pairing
  • G:U pairs allowed in the seed

  • Homepage

    Publication
    Jan. 27, 2015
    Citations: 13
    31 MMIA MMIA integrates microRNA and mRNA expression data with predicted microRNA target information for analyzing microRNA-associated phenotypes and biological functions by Gene Set Enrichment Analysis. 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. This novel web server provides users with miRNA-mRNA expression data combined analysis tools and broad gene sets. /
  • human
  • seed match
  • conservation
  • free energy
  • site accessibility
  • target-site abundance
  • 3' compensatory pairing
  • G:U pairs allowed in the seed
  • local AU content
  • HMM

  • Homepage

    Publication
    May 6, 2009
    Citations: 74
    32 MRmicroT MR-microT is a MapReduce-based implementation of microT target prediction method. It provides near-real time predictions for custom miRNA sequences. /
  • mouse
  • human
  • seed match
  • conservation
  • free energy
  • site accessibility
  • G:U pairs allowed in the seed

  • Homepage

    Publication
    June 30, 2014
    33 MTide MTide is an integrated pipeline designed to parse sRNA-seq and degradome data for miRNA-target identification in plant. It can quantify the known miRNA expression and identify novel miRNA from sRNA-seq data, identify the target of miRNA from degradome data signature, predict target of miRNA precisely, prioritize predicted target according to GO similarity to known or validated target, and identify the expressed miRNA between two samples. /
  • plants
  • seed match
  • conservation
  • free energy
  • 3' compensatory pairing
  • G:U pairs allowed in the seed
  • degradome seq analysis

  • Homepage

    Publication
    Sept. 24, 2014
    Citations: 15
    34 MultiMiTar 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 result of using high quality negative examples and selection of biologically relevant miRNA-targeting site context specific features. The features are selected by using a novel feature selection technique AMOSA-SVM, that integrates the multi objective optimization technique Archived Multi-Objective Simulated Annealing (AMOSA) and SVM. /
  • human
  • seed match
  • site accessibility
  • target-site abundance
  • machine learning
  • 3' compensatory pairing
  • G:U pairs allowed in the seed
  • local AU content
  • Archived Multi-Objective Simulated Annealing

  • Homepage

    Publication
    Sept. 15, 2011
    Citations: 13
    35 Oasis 2.0 Oasis is a web application that allows for the fast and flexible online analysis of small-RNA-seq (sRNA-seq) data. Oasis’ exclusive selling points are a differential expression module that allows for the multivariate analysis of samples, a classification module for robust biomarker detection and an advanced programming interface that supports the batch submission of jobs. Both modules include the analysis of novel miRNAs, miRNA targets and functional analyses including GO and pathway enrichment. /
  • human
  • mouse
  • fly
  • fish
  • worm
  • chicken
  • rat
  • other animals (selectable)
  • seed match
  • conservation
  • free energy
  • G:U pairs allowed in the seed

  • Homepage

    Publication
    Feb. 19, 2015
    Citations: 19
    36 P-TAREF p-TAREF refines the process of microRNA target identification through incorporation of local interaction information for microRNA and target region in the target sequence as well as estimates the candidature of being a true microRNA target on the basis of intrinsic sequence property around the target site determined by varying dinculeotide density profile. Also by considering dinculeotide density we incorporate the nearest neighbor approach of RNA structure determination. /
  • plants
  • seed match
  • conservation
  • free energy
  • target-site abundance
  • machine learning
  • 3' compensatory pairing
  • G:U pairs allowed in the seed

  • Homepage

    Publication
    Dec. 29, 2011
    Citations: 8
    37 PicTar 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. /
  • vertebrates
  • fly
  • worm
  • seed match
  • conservation
  • free energy
  • target-site abundance
  • HMM

  • Homepage

    Publication
    April 3, 2005
    Citations: 1766
    38 PITA PITA offers a brand new view on the miRNA target prediction. The main assumption is based on the fact the mRNA structure plays a role in target recognition by thermodynamically promoting or disfavoring the interaction. /
  • human (online)
  • fly (online)
  • mouse (online)
  • worm (online)
  • animals (local)
  • seed match
  • free energy
  • site accessibility
  • target-site abundance
  • G:U pairs allowed in the seed

  • Homepage

    Publication
    Sept. 23, 2007
    Citations: 862
    39 psRNATarget psRNATarget, a plant small RNA target analysis server, which features two important analysis functions: 1) reverse complementary matching between miRNA and target transcript using a proven scoring schema, and 2) target site accessibility evaluation by calculating unpaired energy (UPE) required to “open” secondary structure around miRNA’s target site on mRNA. PsRNATarget incorporates recent discoveries in plant miRNA target recognition, e.g. it 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. /
  • plants
  • seed match
  • site accessibility
  • target-site abundance
  • it distinguishes translational and post-transcriptional inhibition

  • Homepage

    Publication
    May 27, 2011
    Citations: 455
    40 psRobot psRobot is designed to analyze batch of plant small RNA data.The online version of psRobot has two modules. The stem-loop small RNA prediction module can identify stem-loop shaped smRNAs, including their expression in major plant smRNA biogenesis gene mutants and smRNA associated protein complexes to give clues to the smRNA generation and functional processes, their genome locations and precursor sequences. The second one, small RNA target prediction module, can return target prediction results of smRNAs, including smRNA target list, target multiplicity, target site conservation and biological data support, such as degradome data and target expression data in small RNA biogenesis mutants. /
  • plants
  • seed match
  • conservation
  • target-site abundance
  • 3' compensatory pairing
  • G:U pairs allowed in the seed

  • Homepage

    Publication
    June 12, 2012
    Citations: 77
    41 RNA22 Rna22, a method for identifying microRNA binding sites and their corresponding heteroduplexes. Rna22 does not relay 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. /
  • animals
  • seed match
  • free energy
  • G:U pairs allowed in the seed
  • sensitivity/specificity settings
  • pattern recognision

  • Homepage

    Publication
    July 26, 2006
    Citations: 636
    42 RNAhybrid 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. /
  • any
  • seed match
  • free energy
  • target-site abundance
  • 3' compensatory pairing
  • G:U pairs allowed in the seed

  • Homepage

    Publication
    July 1, 2006
    Citations: 371
    43 sPARTA A powerful tool for plant miRNA target prediction and PARE validation. It can search for targets in unannotated genomic regions, which is useful to discover novel regulatory modules, independent of genome annotations that may be incomplete. /
  • plants
  • seed match
  • target-site abundance
  • G:U pairs allowed in the seed
  • degradome seq analysis

  • Homepage

    Publication
    Aug. 12, 2014
    Citations: 16
    44 sRNAtoolbox 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 sRNAtoolbox is sRNAbench, which allows the expression profiling and prediction of novel microRNAs in deep sequencing experiments. The other tools can be either launched on sRNAbench results, or independently using the appropriate file formats. /
  • human
  • mouse
  • rat
  • chicken
  • fly
  • fish
  • viruses
  • plants (selectable)
  • bacteria
  • 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

  • Homepage

    Publication
    May 27, 2015
    Citations: 46
    45 STarMir STarMir is a tool for predicting potential binding sites for one or multiple microRNAs (miRNA) in a target RNA sequence (typically mRNA). It is based on the logistic prediction models developed with miRNA binding data from crosslinking immunoprecipitation (CLIP) studies. Each of the candidate sites is assigned a logistic probability as a measure of confidence in the predicted site. /
  • any
  • seed match
  • free energy
  • site accessibility
  • 3' compensatory pairing
  • G:U pairs allowed in the seed
  • local AU content
  • CLIP-based

  • Homepage

    Publication
    May 6, 2014
    Citations: 19
    46 submiRine An open-source software package for predicting microRNA target site variants (miR-TSVs) from clinical genomic data sets that measure miRNA expression, gene expression, and genotype. The main benefits of SubmiRine are that it allows for de novo prediction of miR-TSVs from custom data sets - such as those that can be generated from large-scale clinical genomics projects - and provides a methodology to prioritize predicted miR-TSVs by their relative probability of being functional. /
  • human
  • seed match
  • conservation
  • site accessibility
  • target-site abundance
  • 3' compensatory pairing
  • local AU content

  • Homepage

    Publication
    March 26, 2015
    Citations: 3
    47 SVMicrO SVMicrO is mammalian miRNA target prediction algorithm, which assumes a 2-stage structure including a site support vector machine (SVM) followed by a UTR-SVM. SMVicrO makes prediction based on 21 optimal site features and 18 optimal UTR features, selected by training from a comprehensive collection of 113 site and 30 UTR features. Comprehensive evaluation of SVMicrO performance has been carried out on the training data, proteomics data, and immunoprecipitation (IP) pull-down data. /
  • mammals
  • 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
    Sept. 22, 2010
    Citations: 25
    48 TaLasso TaLasso algorithm combines the information of sequence databases with mRNA and miRNA expression to quantify the down-regulation between miRNAs and their putative targets. /
  • human
  • seed match
  • conservation
  • free energy
  • site accessibility
  • target-site abundance
  • 3' compensatory pairing
  • G:U pairs allowed in the seed
  • local AU content
  • miRNA & mRNA expression (needed)
  • HMM

  • Homepage

    Publication
    Feb. 14, 2012
    Citations: 21
    49 TAPIR TAPIR is designed for the prediction of plant microRNA targets. This web 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. /
  • plants
  • seed match
  • free energy
  • 3' compensatory pairing
  • G:U pairs allowed in the seed

  • Homepage

    Publication
    April 28, 2010
    Citations: 62
    50 Target-align A Smith-Waterman-like alignment tool was developed 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. Important parameters, such as maximum mismatches and maximum consecutive mismatches between miRNAs and their targets, were also used for filtering the optimal local alignments. Almost all of the parameters in this alignment tool can be adjusted by users. Target-align can identify multi-target sites as well potential for non-cleaved targets sites by change the default settings. /
  • plants
  • seed match
  • 3' compensatory pairing
  • G:U pairs allowed in the seed

  • Homepage

    Publication
    Oct. 7, 2010
    Citations: 23
    51 TargetMiner A robust tool for microRNA target prediction with systematic identification of negative examples. TargetMiner is a support vector machine (SVM)-based classifier. /
  • 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

  • Homepage

    Publication
    Aug. 19, 2009
    Citations: 63
    52 TargetRank 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. /
  • human
  • mouse
  • seed match
  • conservation
  • target-site abundance
  • local AU content

  • Homepage

    Publication
    Sept. 5, 2007
    Citations: 143
    53 TargetRNA2 TargetRNA2 is a web server that identifies mRNA targets of sRNA regulatory action in bacteria. As input, TargetRNA2 takes the sequence of an sRNA and the name of a sequenced bacterial replicon. When searching for targets of RNA regulation, TargetRNA2 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 mRNA target. /
  • bacteria
  • seed match
  • conservation
  • free energy
  • site accessibility
  • 3' compensatory pairing
  • G:U pairs allowed in the seed

  • Homepage

    Publication
    April 21, 2014
    Citations: 38
    54 TargetScan TargetScan predicts biological targets of miRNAs by searching for the presence of 8mer, 7mer, and 6mer sites that match the seed region of each miRNA. As an option, only conserved sites are predicted. Also identified are sites with mismatches in the seed region that are compensated by conserved 3' pairing and centered sites. In mammals, predictions are ranked based on the predicted efficacy of targeting as calculated using cumulative weighted context++ scores of the sites. As an option, predictions are also ranked by their probability of conserved targeting. TargetScanHuman considers matches to human 3' UTRs and their orthologs, as defined by UCSC whole-genome alignments. Conserved targeting has also been detected within open reading frames (ORFs). Compared to previous releases, Release 7 uses an improved method to predict targeting efficacy (the context++ model), uses 3' UTR profiles that indicate the fraction of mRNA containing each site, and uses updated miRNA families. /
  • human
  • mouse
  • fly
  • worm
  • fish
  • 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
    Aug. 12, 2015
    Citations: 667
    55 TargetSpy TargetSpy, 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. It does not rely on evolutionary conservation, which allows the detection of species-specific interactions and makes TargetSpy suitable for analyzing unconserved genomic sequences. /
  • human
  • mouse
  • chicken
  • rat
  • fly
  • free energy
  • site accessibility
  • machine learning
  • 3' compensatory pairing

  • Homepage

    Publication
    May 28, 2010
    Citations: 46
    56 TarPmiR Approach for miRNA target site prediction which includes 13 different features. /
  • human
  • seed match
  • conservation
  • free energy
  • site accessibility
  • machine learning
  • 3' compensatory pairing
  • local AU content
  • m/e motif
  • the total number of paired positions
  • the length of the target mRNA region
  • the lenght of the largest consecutive pairings
  • and two others

  • Homepage

    Publication
    May 20, 2016
    Citations: 6
    57 UEA sRNA Workbench The UEA sRNA workbench is a simple to use, downloadable sRNA software package based on algorithms developed for the original UEA sRNA Toolkit that will perform a complete analysis of single or multiple-sample small RNA datasets from both plants and animals to identify interesting landmarks (such as detection of novel micro RNA sequences) or other tasks such as profiling small RNA expression patterns in genetic data. /
  • plants
  • animals
  • viruses
  • seed match
  • 3' compensatory pairing
  • G:U pairs allowed in the seed
  • Rule-Based Complementarity Search
  • degradome seq analysis

  • Homepage

    Publication
    May 24, 2012
    Citations: 90
    58 wapRNA wapRNA provides an integrated tool for RNA sequence, refers to the use of High-throughput sequencing technologies to sequence cDNAs in order to get information about a sample's RNA content. wapRNA provides researchers with efficient ways to measure RNA sequence experimentally, allowing them to get information such as how different alleles of a gene are expressed, detect post-transcriptional mutations or identifying gene fusions, annotate the known miRNAs or predict the news and so on.  /
  • human
  • mouse
  • rat
  • worm
  • fly
  • chicken
  • worm
  • fish
  • other animals (selectable)
  • any (local)
  • seed match
  • conservation
  • free energy
  • target-site abundance
  • 3' compensatory pairing
  • G:U pairs allowed in the seed

  • Homepage

    Publication
    Sept. 6, 2011
    Citations: 23
    59 WMD3 WMD3 - Web app for the automated design of artificial plant microRNAs. Platform requires only selection of favorite candidates according to a small set of criteria. It is designed to optimize both intrinsic small RNA properties as well as specificity within the given transcriptome. /
  • plants
  • seed match
  • free energy
  • site accessibility

  • Homepage

    Publication
    Feb. 4, 2008
    Citations: 156