miRNA主要通过与目的mRNA的结合,促使mRNA降解或阻碍其翻译,从而抑制目的基因的表达。本文根据(tools4mirs.org)汇总的60余款工具分享给大家。

BcmicrOBcmicrO 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.humanHomepage

Publication
Dec. 17, 2012
Citations: 9
BioVLAB-MMIA-NGSBioVLAB-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)
Homepage

Publication
Sept. 29, 2014
Citations: 7
CleaveLand4CleaveLand 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.anyHomepage

Publication
Nov. 18, 2008
Citations: 237
ComiRComiR (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
Homepage

Publication
Dec. 20, 2012
Citations: 21
comTARcomTAR 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.plantsHomepage

Publication
March 14, 2014
Citations: 4
CPSSCPSS 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
Homepage

Publication
May 9, 2012
Citations: 22
DeAnnIsoDeAnnIso, 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
Homepage

Publication
May 13, 2016
Citations: 18
DIANA-microT-CDSDIANA-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
Homepage

Publication
May 16, 2013
Citations: 422
ElMMo3A 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
Homepage

Publication
March 1, 2007
Citations: 155
GUUGleGUUGle 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.anyHomepage

Publication
Jan. 10, 2006
Citations: 18
homoTargetCombined 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.humanHomepage

Publication
Nov. 19, 2012
Citations: 8
iMiriMir 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.anyHomepage

Publication
Dec. 13, 2013
Citations: 26
IntaRNAIntaRNA 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.anyHomepage

Publication
Oct. 21, 2008
Citations: 211
isomiR2FunctionsomiR2Function 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.plantsHomepage

Publication
March 21, 2017
Citations: 5
LeARN/smallAA platform based on LeARN, dedicated to analyse data generated by RNAseq small RNA projects.anyHomepage

Publication
Jan. 14, 2008
Citations: 8
MAGIMAGI 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.humanHomepage

Publication
June 6, 2014
Citations: 10
MAGIA2MAGIA2 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
Homepage

Publication
May 21, 2012
Citations: 62
MicroInspectorMicroInspector 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)Homepage

Publication
July 1, 2005
Citations: 95
MicroTarMicroTar 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 packageanimalsHomepage

Publication
Dec. 18, 2006
Citations: 37
miRabelmiRabel is a efficient tool for the prediction of miRNA target mRNAs and their associated biological functions. miRabel aggregated all human results of four important prediction algorithms (miRanda, PITA, SVmicrO, and TargetScan) showing additional characteristics in order to rerank them into a single list.humanHomepage

Publication
Jan. 28, 2020
Citations: 14
miRandamiRanda 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.anyHomepage

Publication
Oct. 5, 2004
Citations: 1489
miRcodeProvides “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.humanHomepage

Publication
June 19, 2012
Citations: 300
miRDBRecently 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
Homepage

Publication
Nov. 5, 2014
Citations: 793
miRmapTo 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
Homepage

Publication
May 28, 2013
Citations: 47
miRror SuiteThe 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
Homepage

Publication
June 6, 2014
Citations: 6
miRTarmiRTar, 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.humanHomepage

Publication
July 26, 2011
Citations: 54
miRTarCLIPFrom 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
Homepage

Publication
Jan. 21, 2013
Citations: 24
mirTools 2.0MirTools 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
plants
any (local)
Homepage

Publication
May 29, 2013
Citations: 36
mirWIPmirWIP 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 methodsWormHomepage

Publication
Aug. 17, 2008
Citations: 102
MIRZAA 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.humanHomepage

Publication
Jan. 20, 2013
Citations: 71
MIRZA-GA 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.humanHomepage

Publication
Jan. 27, 2015
Citations: 26
MMIAMMIA 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.humanHomepage

Publication
May 6, 2009
Citations: 84
MRmicroTMR-microT is a MapReduce-based implementation of microT target prediction method. It provides near-real time predictions for custom miRNA sequences.mouse
human
Homepage

Publication
June 30, 2014
MTideMTide 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.plantsHomepage

Publication
Sept. 24, 2014
Citations: 25
MultiMiTarMultiMiTar 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.humanHomepage

Publication
Sept. 15, 2011
Citations: 16
Oasis 2.0Oasis 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
Homepage

Publication
Feb. 19, 2015
Citations: 30
P-TAREFp-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.plantsHomepage

Publication
Dec. 29, 2011
Citations: 12
PicTarPicTar 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
Homepage

Publication
April 3, 2005
Citations: 2046
PITAPITA 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)
Homepage

Publication
Sept. 23, 2007
Citations: 1099
psRNATargetpsRNATarget, 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.plantsHomepage

Publication
May 27, 2011
Citations: 644
psRobotpsRobot 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.plantsHomepage

Publication
June 12, 2012
Citations: 170
RNA22Rna22, 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.animalsHomepage

Publication
July 26, 2006
Citations: 834
RNAhybridRNAhybrid 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.anyHomepage

Publication
July 1, 2006
Citations: 640
sPARTAA 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.plantsHomepage

Publication
Aug. 12, 2014
Citations: 30
sRNAtoolboxsRNAtoolbox 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
bacteria
other animals
Homepage

Publication
May 27, 2015
Citations: 93
STarMirSTarMir 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.anyHomepage

Publication
May 6, 2014
Citations: 34
submiRineAn 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.humanHomepage

Publication
March 26, 2015
Citations: 5
SVMicrOSVMicrO 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.mammalsHomepage

Publication
Sept. 22, 2010
Citations: 36
TaLassoTaLasso algorithm combines the information of sequence databases with mRNA and miRNA expression to quantify the down-regulation between miRNAs and their putative targets.humanHomepage

Publication
Feb. 14, 2012
Citations: 30
TAPIRTAPIR 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.plantsHomepage

Publication
April 28, 2010
Citations: 101
Target-alignA 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.plantsHomepage

Publication
Oct. 7, 2010
Citations: 26
TargetMinerA robust tool for microRNA target prediction with systematic identification of negative examples. TargetMiner is a support vector machine (SVM)-based classifier.humanHomepage

Publication
Aug. 19, 2009
Citations: 82
TargetRankTargetRank 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
Homepage

Publication
Sept. 5, 2007
Citations: 171
TargetRNA2TargetRNA2 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.bacteriaHomepage

Publication
April 21, 2014
Citations: 63
TargetScanTargetScan 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
Homepage

Publication
Aug. 12, 2015
Citations: 2467
TargetSpyTargetSpy, 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
Homepage

Publication
May 28, 2010
Citations: 64
TarPmiRApproach for miRNA target site prediction which includes 13 different features.humanHomepage

Publication
May 20, 2016
Citations: 43
UEA sRNA WorkbenchThe 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
Homepage

Publication
May 24, 2012
Citations: 125
wapRNAwapRNA 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 any (local)
Homepage

Publication
Sept. 6, 2011
Citations: 26
WMD3WMD3 – 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.plantsHomepage

Publication
Feb. 4, 2008
Citations: 203

参考资料:

1.https://tools4mirs.org/software/target_prediction/