Tools4miRs - Target Prediction

Target Prediction
Computational methods for potential miRNA targets selection

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#	Name	Description	Online/Local	Organism Specific	Algorithm Features	References
1	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: 8
2	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: 312
3	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: 22
4	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: 5
5	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: 25
6	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: 20
7	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: 611
8	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: 176
9	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: 23
10	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: 259
11	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: 10
12	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
13	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: 44
14	miRabel	miRabel 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.	/	human		Homepage Publication Jan. 28, 2020 Citations: 50
15	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: 1807
16	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: 419
17	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: 1006
18	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: 72
19	miRTar2GO	miRTar2GO is a method that predicts miRNA targets by allocating CLIPed regions of the mRNA 3' UTRs to miRNA seed regions.	/	human	seed match site accessibility mRNA differential expression	Homepage Publication April 7, 2017 Citations: 4
20	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: 40
21	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: 31
22	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
23	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: 41
24	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: 19
25	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: 33
26	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: 17
27	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: 2219
28	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: 1251
29	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: 782
30	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: 245
31	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: 990
32	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: 900
33	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: 36
34	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: 118
35	sRNAtools	sRNAtools can be used to identify and functionally annotate diverse kinds of sncRNA for up to 21 model species (including human, mouse, Arabidopsis, rice, etc.), including (i) profiling of miRNAs, Piwi-interacting RNA (piRNAs), piRNA-producing loci (piRNA cluster), tRNAs, natsiRNA, small nuclear RNAs (snRNAs), small nucleolar RNAs (snoRNAs) and rRNAs and (ii) discovering isomiRs, novel miRNAs, tRFs, plant-specific 24-nt siRNAs and phasiRNAs. sRNAtools also provides web-based approaches to detect sncRNAs in multiple transcriptomes.	/	plants animals mouse fish worm rat fly human	seed match conservation free energy G:U pairs allowed in the seed	Homepage Publication Jan. 18, 2021 Citations: 21
36	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: 51
37	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: 9
38	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: 45
39	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: 38
40	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: 143
41	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: 31
42	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: 103
43	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: 193
44	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: 93
45	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: 3862
46	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: 76
47	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: 83
48	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: 149
49	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: 26
50	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: 235

Target PredictionComputational methods for potential miRNA targets selection

Target Prediction
Computational methods for potential miRNA targets selection